The biology of habitat dominance; can microbes behave as weeds?

1As the collective metabolism and ecological activities of microorganisms determine the health and sustainability of life on Earth it is essential to understand the function of both individual microbes and in their communities. The cellular systems of an insignificant portion of microbial species have been intensively characterized at the levels of biochemistry, cell biology, genomics and systems biology; and a substantial body of (top-down) studies has been published in the field of microbial ecology in relation to species interactions, community succession and environmental metagenomics. There are, however, some fundamental questions that remain unanswered in relation to the behaviour of microbial species within communities: what type of biology, for instance, enables microbes to dominate entire communities and their habitats and thereby determine levels of biodiversity in specific environments?

2Plant species that primarily inhabit freshly disturbed habitats – known as weeds – are characterized by vigorous growth; tolerance to multiple stresses; exceptional reproduction, dispersal and survival mechanisms; a lack of specific environmental requirements; production of phytotoxic chemicals; and/or other competitive strategies (Table 1). The biology of plant weeds, including their phenotypic and genetic traits, has been the subject of extensive study over the past 100 years and is now relatively well characterized (Table 1; Long,; Anderson,; Salisbury,; Hill,; Mack et al.,; Schnitzler and Bailey,; Bakker et al.,; Chou,; Wu et al.,; Liberman et al., ). We hypothesize that weed biology is also pertinent to microbial species, but that the defining characteristic of microbial weeds is their ability to dominate their respective communities. In the field of plant ecology it is open habitats (such as freshly exposed fertile soil) that facilitate the emergence of weed species both within specific ecosystems and across evolutionary timescales. We propose that weed behaviour is equally prevalent in some microbial habitats, that open microbial habitats promote the emergence of microbial weed species, and that microbial weed biology represents a potent ecological and evolutionary mechanism of change for some microbial species and their communities.

3This article focuses on the following questions: (i) what types of substrate or environment facilitate the emergence of dominant microbial species, (ii) are there archetypal weed species that can consistently dominate microbial communities, (iii) what are the stress biology, nutritional strategies, energy-generating capabilities, antimicrobial activities and other competitive strategies of microbial weeds, (iv) which components and characteristics of microbial cells form the mechanics of weed biology, (v) what are the properties of open (microbial) habitats that promote the emergence of weed species, and (vi) how are microbial weeds conceptually distinct from plant weeds, and other ecophysiological groups of microorganism?

4The microbial diversity of specific habitats, as well as that of Earth's entire biosphere, is an area of intensive scientific interest that has implications within the fundamental sciences and for drug discovery, biotechnology and environmental sustainability. Biodiversity provides the material basis for competition between microbial taxa, species succession in communities, and other aspects of microbial ecology that collectively impact the evolution of microbial species (Cordero et al., ). We believe that certain microbes are genetically, and thus, metabolically hard-wired to dominate communities (monopolizing available resources and space) and thereby reduce biodiversity within the habitat. Microbial communities can reach a stationary-phase or climax condition with a relatively balanced species composition (McArthur, ). However whether tens or thousands of microbial species are initially present (Newton et al., ) the community can become dominated by a single – or two to three – species (Fig. 1; Table S1; Randazzo et al.,; Cabrol et al., ). For example the indigenous microflora of olives is comprised of significant quantities of phylogenetically diverse species such as Aureobasidium pullulans, Candida spp., Debaryomyces hansenii, Metschnikowia pulcherrima, Pichia guilliermondii, Pichia manshurica, Rhodotorula mucilaginosa and Zygowilliopsis californica (Fig. 1Bi; Nisiotou et al., ). Nisiotou and colleagues found that species succession and the stationary-phase community during olive fermentations are determined by one dominating genus, Pichia, three species of which account for almost 100% of the community by 35 days (see Fig. 1Biii). The most prevalent of these, Pichia anomala, is a microbial generalist that is not only able to inhabit ecologically and nutritionally distinct environments (e.g. palm sugar, cereals, silage, oil-contaminated soils, insects, skin, various marine habitats; see Walker, ) but can also dominate the communities that develop in diverse habitat types (Table S1; Tamang,; Walker, ). Studies of Pecorino Crotonese cheese fermentations reveal that, even though the curd contains > 300 bacterial strains, the community is eventually dominated by Lactobacillus rhamnosus (Randazzo et al., ).

5Species that are able to dominate communities that develop in open habitats are not restricted to copiotrophs, generalists or any established ecophysiological grouping of microorganism (Table S1). Furthermore dominating species span the Kingdoms of life and, collectively, can be observed in most segments of the biosphere; from bioaerosols to solar salterns, oceans and freshwater to sediments and soils, the phyllosphere and rhizosphere, to those with molar concentrations of salts or sugars (see Table S1). The phenomenon can also be observed during food-production, food-spoilage and waste-decomposition processes where resource-rich habitats are available for colonization (see Table S1). The materials present in and the microbes living on these substrates are ultimately derived from the natural environment so community successions resulting in single-species dominance are likely to be commonplace in comparable open habitats within natural ecosystems (Table S1; Senthilkumar et al.,; Nisiotou et al.,; Reynisson et al.,; Rajala et al., ). Microbial weed species are able to dominate open habitats that progress to a closed condition (e.g. fermenting fruit juice) as well as those that remain in a more or less perpetually open state (e.g. the surface-fluid film of sphagnum moss and rhizosphere of plants growing in moist soils); see Table S1. Weeds emerge in habitats where competing cells are in close proximity (such as biofilms; Table S1; Rao et al., ) as well as those where there is limited mechanical contact between cells, such as the aqueous habitats of planktonic species (Table S1; Collado-Fabbri et al.,; Trigal et al.,; Leão et al., ); and in both extreme and non-extreme environments (Table S1). Some microbes emerge as a/the dominating species in diverse types of habitat including specialists such as Lactobacillus (that do so, in part, by acidifying their environment) and generalists such as Aspergillus, Pichia and Pseudomonas species (Table S1; Steinkraus,; Tamang, ). For weed species such as Saccharomyces cerevisiae (high-sugar environments), Haloquadratum walsbyi (aerobic, hypersaline brines), and Gonyostomum semen and Microcystis aeruginosa (eutrophic freshwater) ability to dominate can be restricted to a specific type of habitat. Most of these microbes do not populate their respective habitat as a one-off or chance event; they can consistently dominate their microbial communities and do so regardless of their initial cell number (Table S1; for P. anomala see Fig. 1; for S. cerevisiae see Pretorius,; Renouf et al.,; Raspor et al.,; for L. rhamnosus see Randazzo et al., ). It is therefore intriguing to consider what combination(s) of traits can give rise to a weed phenotype.

6During habitat colonization, even in apparently stable, homogenous environments such as sugar-based solutions, there are dynamic/drastic changes in stressor concentrations, antimicrobials and stress parameters (D'Amore et al.,; Hallsworth,; Eshkol et al.,; Fialho et al.,; see also below). As a result of these fluctuations microbes are exposed to multiple stresses some of which present potentially lethal challenges to the cell. In soil and sediments, for example the water activit can oscillate from low to high and high to low; these substrates typically cycle between desiccation and rehydration and are subjected to changes in solar radiation, temperature, and even freezing and thawing. Soils and sediments can be physically heterogeneous such that water availability, solute concentrations and other stress parameters exhibit profound spatial fluctuations. In addition, intracellular metabolites and extracellular substances (of both biotic and abiotic origin) impose stresses due to ionic, osmotic, chaotropic, hydrophobic and other activities of solutes (see Brown,; Hallsworth et al.,;; Lo Nostro et al.,; Bhaganna et al.,; Chin et al., ). On the one hand resilience to stress undoubtedly contributes to competitive ability but on the other a vigorous growth phenotype and reinforced stress biology also require extraordinary levels of energy generation. Furthermore, microbes that can achieve a greater net gain in energy than competing species will have an ecological advantage (Pfeiffer et al., ). Here we suggest that species able to dominate microbial communities are exceptionally well equipped to resist the effects of multiple stress parameters, and that many have high-efficiency energy-generation systems.

7We tested the hypothesis that microbial weeds are exceptionally tolerant to habitat-relevant stresses for two species; the soil bacterium Pseudomonas putida (Table 2) and the specialist yeast S. cerevisiae (see below). Environments in which P. putida is a major ecological player (Table S1) typically contain an array of chemically diverse aromatics and hydrocarbons that induce chaotropicity-mediated stresses (Hallsworth et al.,; Bhaganna et al.,; Cray et al., ). This bacterium is not only renowned for its metabolic versatility, but is also known for its tolerance to specific solutes and solvents (Hallsworth et al.,; Domínguez-Cuevas et al.,; Bhaganna et al., ). We compared the biotic windows for growth of P. putida for eight mechanistically distinct classes of stress using 37 habitat-relevant substances (Table 2). This bacterium was able to tolerate all substances within each group of stressor; this is the first data set to demonstrate that a mesophilic bacterium can tolerate the following combination of stresses: up to 4–11 mM hexane, toluene and benzene; 8–115 mM concentrations of aromatic, chaotropic solutes; 300–825 mM chaotropic salts; 1300–2160 mM sugars or polyols; 200–750 mM kosmotropic salts; and considerable levels of matric stress (Brown, ) generated by kosmotropic polysaccharides (Table 2). The P. putida tolerance limits to highly chaotropic substances and hydrophobic compounds were superior to those of other microbes (including extremophiles and polyextremophiles; Table 2; Hallsworth et al.,; Bhaganna et al., ). Whereas prokaryotes are generally less tolerant to solute stress than eukaryotes (Brown, ), the resilience to this array of mechanistically diverse solute stresses (Table 2) has neither been equalled nor been surpassed by any microbial species to our knowledge.

8Pseudomonas putida is able to avoid contact with or prevent accumulation of stressors by using solvent-efflux pumps and synthesizing extracellular polymeric substances to form a protective barrier (Table 3). This bacterium also utilizes highly efficient macromolecule-protection systems that are upregulated in response to multiple environmental stresses including between 10 and 20 protein-stabilization proteins, oxidative-stress responses, and upregulation of energy generation and overall protein synthesis (Table 3). Furthermore, P. putida can synthesize an array of compatible solutes including betaine, proline, N-acetylglutaminylglutamine amide, glycerol, mannitol and trehalose (Table 3). Individual compatible solutes are unique in their physicochemical properties, interactions with macromolecular systems and functional efficacy for specific roles within the cell (e.g. see Chirife et al.,; Crowe et al.,; Brown,; Hallsworth and Magan,; Yancey,; Bhaganna et al.,; Bell et al., ). Microbes that are able to selectively utilize/deploy any substance(s) from a range of diverse compatible solutes have enhanced tolerance to diverse stresses (e.g. Hallsworth and Magan,; Bhaganna et al., ). The range of compatible solutes utilized by P. putida may be unique for a bacterium (see Brown, ) and can confer tolerance to diverse stresses including those imposed by chaotropes and hydrocarbons (Bhaganna et al., ).

9The exceptionally wide growth-windows of Aspergillus species in relation to a number of stress parameters correlate with their ability to dominate communities in both extreme and non-extreme (but physicochemically dynamic) environments including soils, plant necromass, saline and very high-sugar habitats (Table S1). At least 20 species of Aspergillus and the closely related genus Eurotium are xerotolerant (Pitt,; Brown, ). Aspergillus penicillioides is capable of hyphal growth and conidial germination down to water activities of 0.647 and 0.68 respectively (Pitt and Hocking,; Williams and Hallsworth, ); Aspergillus echinulatus can germinate down to 0.62 (Snow, ). Halotolerant species such as Aspergillus wentii can grow on the highly chaotropic salt guanidine-HCl at a higher concentration than any other microbe; up to 930 mM (≡ 26.5 kJ g−1 chaotropic activity; Hallsworth et al., ) and, along with Aspergillus oryzae, up to ∼ 4 M NaCl or KCl (Hallsworth et al., ). Aspergillus (and Eurotium) strains are capable of reasonable growth rates close to 0°C (Chin et al., ), and some reports suggests that the biotic windows for some Aspergillus species ultimately fail at ≤ −18°C (Vallentyne,; Siegel and Speitel, ). Whereas a number of comparable fungal genera show moderate levels of stress tolerance, Aspergillus species generally out-perform their competitors and top numerous league tables for ascomycete stress tolerance (see Pitt,; Wheeler and Hocking,; Williams and Hallsworth, ).

10Studies of seven Aspergillus species have revealed a number of genome modifications within this genus that reinforce both primary metabolism and energy generation (Table 3; Flipphi et al., ). These include gene duplications for key enzymes that control metabolic flux, such as pyruvate dehydrogenase, citrate synthase, aconitase, and malate dehydrogenase that enhance glycolysis and the TCA cycle (Flipphi et al., ). There is evidence that, at the low water activities (high osmotic pressures) associated with very high-salt and high-sugar habitats, the biotic window of xerophilic fungi fail due to the prohibitive energy expenditure required to prevent the high levels of intracellular glycerol from leaking out of the membrane (Hocking, ). The adaptability and competitive ability of Aspergillus species (most of which can also proliferate under non-extreme conditions) may be attributed, in part, from enhanced energy-generating capability. Aspergillus species (like many fungi) can utilize a range of polyols – as well as trehalose – as compatible solutes based on their individual strengths as protectants against osmotic stress, desiccation rehydration, chaotropes etc. (Crowe et al.,; Brown,; Hallsworth et al., ). Aspergillus and Eurotium strains can also accumulate chaotropic sugars from the medium, or preferentially synthesize and accumulate chaotropic glycerol, in order to enhance growth at temperatures below ∼ 10°C (Chin et al.,; see also below).

11Salinibacter ruber is a halophilic bacterium found in high numbers at molar salt concentrations in aerobic aquatic habitats that are otherwise more densely populated by archaeal than bacterial species. Unusually for a bacterium, S. ruber takes in ions to use as compatible solutes and thereby avoids synthesis of organic compatible solutes that would be energetically unfavourable in environments of > 1 M NaCl (Oren, ) and has evolved intracellular proteins that are both structurally stable and catalytically functional in the cytosol at high ionic strength (Table 3). Salinibacter ruber (as well as the alga Dunaliella salina and yeast R. mucilaginosa) accumulates carotenoids in response to light which can protect against oxidative stress that is a potential hazard in salterns exposed to high levels of ultraviolet (Table 3). Haloquadratum walsbyi, an Archaeon that is also a dominant player in saltern communities (Table S1), also uses the ‘salt-in’ compatible-solute strategy, and – along with S. ruber – has light-activated protein pumps that generate proton-motive force and thereby boost energy generation (Table 3). In addition, H. walsbyi is unusually tolerant to the chaotropic salt MgCl2 that can reach high concentrations in evaporate ponds (Hallsworth et al.,; Bardavid et al., ). Dunaliella salina is also highly prevalent in saline habitats that (unusually for an alga) can successfully compete with the multitude of halophilic Archaea found in 5 M NaCl environments (see later; Table S1). This alga preferentially utilizes glycerol as a compatible solute, is able to accumulate glycerol to molar concentrations (6–7 M; see Bardavid et al., ), and has low membrane permeability to this compatible-solute thus aiding retention (Bardavid et al., ).

12Glycerol is unique in its ability to maintain the flexibility of macromolecular structures under conditions that would otherwise cause excessive rigidification, e.g. molar concentrations of NaCl, or low temperature (Back et al.,; Hallsworth et al.,; Williams and Hallsworth,; Chin et al., ). Species able to grow at low or subzero temperatures (e.g. Aspergillus, Cryptococcus, Rhodotorula species, including R. mucilaginosa) either primarily use glycerol as a compatible solute or preferentially accumulate this chaotrope at low temperature (Table 3; Lahav et al.,; Chin et al., ). Rhodotorula mucilaginosa is able to colonize – and frequently dominates – diverse substrates/environments including saline and non-saline soils, aquatic habitats (both liquid- and ice-associated), the acidic surface-film of sphagnum moss (as well as other plant tissues) and various surfaces within the human body and other animals (Table S1; Egan et al.,; Trindade et al.,; Vital et al.,; Lahav et al.,; Lisichkina et al.,; Buzzini et al.,; Perniola et al.,; Goyal et al.,; Turk et al.,; Kachalkin and Yurkov, ). This ability is coupled with an exceptional level of tolerance to multiple stresses: R. mucilaginosa is (highly unusual for a yeast) a polyextremophile that is psychrophilic, highly salt-tolerant, and can growth over the majority of the pH range known to support microbial life (i.e. < 2 and > 10, see Table 3; Lahav et al., ).

13Some microbial habitats such as fruits that have been disconnected from the vascular system (and immune responses) of the parent plant have a favourable water activity and high nutrient availability and are therefore potentially habitable by a wide range of microbes (Ragaert et al., ). As the microbial community develops on a detached fruit (or in apple or grape musts; see Table S1) there can be changes in the composition and concentration of sugars, osmolarity, water activity, ethanol concentration (and that of other antimicrobials), pH and other environmental factors that are severe enough to inhibit or eliminate most members of the original microflora (see Brown,; Hallsworth,; de Pina and Hogg,; Pretorius,; Bhaganna et al., ). The yeast S. cerevisiae that is relatively scarce in natural habitats (and even when present forms a quantitatively insignificant component of the natural community; Renouf et al.,; Raspor et al., ) is unsurpassed in its ability to emerge to dominate high-sugar habitats at water activities above 0.9 (Table S1; Hallsworth,; Pretorius, ). We therefore compared its tolerance towards a range of habitat-relevant stressors with those of 12 other yeasts that occur at the insect–flower interface, on plant tissues, and/or are environmentally widespread (Fig. 2; Table 4). This experiment revealed that S. cerevisiae has a more vigorous growth phenotype and more robust stress tolerance than the other species tested with the exception of two species of Pichia, another genus characterized by weed-like traits (see Fig. 2; Table 4). Stress phenotypes of the yeasts assayed were compared on the basis of stressor type and mechanistically distinct stress-parameters in order to assess resilience to both the degree and diversity of environmental challenges (Table 4). Under the assay conditions it was the three S. cerevisiae strains, Pichia (Kodamaea) ohmeri and Pichia sydowiorum that exhibited the greatest tolerance to the widest range of solute-imposed stresses (Table 4). Other species studied were slow growers, have specific environmental requirements (e.g. the halotolerant D. hansenii and Hortaea werneckii), and/or otherwise lacked the capacity for vigorous growth on the high-sugar substrate at 30°C (see Fig. 2). Generally S. cerevisiae strains were fast-growing, xerotolerant, and highly resistant to chaotrope-induced, osmotic, matric and kosmotrope-induced stresses and are known to be acidotolerant and capable of growth over a wide temperature range, from ∼0°C to 45°C (Fig. 2A and B; Table 4). Although Pichia species can produce ethanol (P. anomala can produce up to 0.36 M ethanol; Djelal et al., ) when growing side by side in high-sugar habitats with S. cerevisiae, Pichia species are unable to tolerate the molar ethanol concentrations that S. cerevisiae can produce (Lee et al., ).

14Saccharomyces cerevisiae is metabolically wired to concomitantly synthesize an antimicrobial chaotrope (ethanol), accumulate a compatible solute (glycerol) that affords protection against this chaotrope (see below), and at the same time generate energy without any loss of ATP-generation efficiency (Table 3): a remarkable phenotype that is coupled with the deployment of other compatible solutes under specific conditions (trehalose and proline). Trehalose, which can reach concentrations of up to 13% dry weight in S. cerevisiae (Aranda et al., ), is highly effective at stabilizing macromolecular structures that are exposed to chaotropic substances (e.g. ethanol, 2-phenylethanol) and enabling cells to survive desiccation–rehydration cycles (Crowe et al.,; Mansure et al., ). The highest reported tolerance to ethanol stress was in S. cerevisiae cells capable of growth and metabolism up to 28% v/v (≡ 20% w/v or 4.3 M; chaotropic activity = 25.3 kJ g−1; Hallsworth,; Hallsworth et al., ) when the medium contained high concentrations of a compatible solute, proline (Thomas et al., ); furthermore of the seven microbes reported to have the highest resistance to other chaotropic substances (including urea, phenol) the majority are weed species including A. wentii, S. cerevisiae, Escherichia coli and P. putida (Hallsworth et al., ).

15The stress mechanisms for numerous types of cellular stress operate at the level of water:macromolecule interactions (Crowe, et al.,; Brown,; Sikkema et al.,; Casadei et al.,; Ferrer et al.,; Hallsworth et al.,; McCammick et al.,; Bhaganna et al.,; Chin et al., ). As front-line stress protectants, compatible solutes (within limits) can therefore mollify stress the inhibitory effects of an indefinite number of stress parameters (see Crowe, et al.,; Brown,; Hallsworth et al.,; Bhaganna et al.,; Chin et al.,; Bell et al., ) but cells also upregulate other protection systems (see also above; Table 3). In S. cerevisiae, an extensive number of genes that code for protein-stabilizing proteins, metabolic enzymes and cellular-organization proteins are regulated by a single promoter – the stress response element (STRE) – which is activated under cellular stress. This regulatory system enables the coordination of an array of stress responses in an energy-efficient manner (Table 3). Numerous studies show that the S. cerevisiae responses to osmotic stress [via the high-osmolarity glycerol-response (HOG) pathway], oxidative stress, and challenges to protein and membrane stability are exceptionally efficient (Table 3; Brown,; Costa et al.,; Hallsworth,; Rodríguez-Peña et al.,; Szopinska and Morsomme, ). In addition to these stress responses, there is evidence that the dynamics of polyphosphate and glycogen metabolism in S. cerevisiae are wired in such a way to boost ATP production (Castrol et al., ), and that the ploidy levels of many strains enhance tolerance towards oxidative and other stresses (Table 3). The energy-generation and energy-conservation strategies employed by S. cerevisiae have apparent parallels in other weed species; for example, analyses of synonymous codon bias in the genomes of fast-growing bacteria including E. coli and Bacillus subtilis suggest that genes associated with energy generation are highly expressed (Karlin et al.,; Table 5; see also above). The enhanced energy efficiency that is apparent in some weed species not only underpins their robust stress biology, but is required to sustain a vigorous growth phenotype and/or to out-grow competitors.

16Efficient cell division and an ability to out-grow competitors are implicit to the emergence of weed species. Species that grow relatively slowly or remain quiescent, and those with specific requirements for a host, a symbiotic partner, or obligate interactions with other microbial species are disadvantaged during community development in open habitats: dominance ultimately results from vigour and – in many habitats – a degree of nutritional versatility (Tables S1 and5). Ability to out-grow competitors is equally important (possibly even more so) for weed species in nutrient-poor and physicochemically extreme habitats that can both select for slow-growing species and limit overall biomass development. Many traits that give rise to an efficient growth phenotype can be found in weed species (Table 5): multiple copies of ribosomal DNA operons that can enhance rates of protein synthesis; transport proteins to scavenge macromolecules thus negating the need for de novo synthesis; high-efficiency DNA polymerase for rapid genome replication; efficient systems to eliminate reactive oxygen species that are a by-product of rapid growth; and polyploidy, aneuploidy and plasmids that can be associated with enhanced stress tolerance, higher growth-rates and increased overall vigour (Table 5). We believe that another key aspect of weed biology for some microbial species is their ability to sequester and store available nutrient and substrate molecules with a high efficiency as an auxiliary energy reserve (see below), to be able to supply daughter cells with nutrients, and simultaneously deprive other microbes of nutritional resources (e.g. Duiff et al.,; Castrol et al.,; Loaces et al.,; Renshaw et al.,; Jahid et al., ). Microbial weeds are highly efficient at nutrient-sequestration and substrate utilization, as well as intracellular storage of these substances (Table 5). For example, fungal siderophores that remove iron from the habitat have been shown to suppress growth of other microorganisms due to iron limitation (Renshaw et al., ).

17Intermittent nutrient availability and low nutrient concentrations are characteristic of many aquatic environments so the ability to scavenge and store, circumvent the requirement for, or strategically utilize scarce and potentially limiting nutrients can greatly enhance the competitive ability of planktonic species. Under phosphate-limiting conditions some aquatic species, including S. ruber, are able to use sulfur-containing glycolipids in place of phospholipids during low phosphate availability (Table 5). The cyanobacterium M. aeruginosa has high-efficiency phosphate-transport systems and accumulates intracellular polyphosphate which is used to maintain activity once extracellular phosphate is depleted (Table 5; Shi et al., ). It is likely that this trait contributes to its weed-like phenotype in Lake Taihu (China) that is a well-studied, phosphate-limited habitat frequently dominated by M. aeruginosa (Shi et al., ). Iron is another potentially limiting nutrient in aquatic habitats. Dunaliella salina utilizes a highly efficient iron-binding protein to take up iron which is then stored in vacuoles (Paz et al., ). Species such as D. salina and H. walsbyi cope with oligotrophic conditions by hyperaccumulating starch and/or lipids such as polyhydroxybutyrate especially when nutrients other than carbon are limiting (Table 5; Bardavid et al., ). One weed species with adaptations to endure low-nitrogen conditions is Mycobacterium smegmatis. This species (as well as other mycobacteria) which can be prevalent in relatively low-nutrient aquatic and non-aquatic habitats (Koch,; Kazda and Falkinham III, ) have biochemical adaptations to enable growth and metabolic activity even when nitrogen concentrations are an order of magnitude lower than those usually required for structural growth (i.e. a C: N ratio of 8:1; Roels,; Behrends et al., ). In addition to nitrogen oligotrophy, M. smegmatis has a DNA polymerase capable of nucleotide processing rates and generation times that are an order of magnitude faster than those of comparable Mycobacterium species (Table 5). Light and/or oxygen are key resources for many planktonic species; 12 genes have been identified that are involved in gas synthesis and storage in species such as M. aeruginosa and H. walsbyi (Table 5). Modelling approaches indicate that buoyancy, which enables the cell to access the upper (well-illuminated, well-oxygenated) section of the water column, plays a key role in habitat dominance by M. aeruginosa (Bonnet and Poulin, ). Studies of H. walsbyi suggest that its peculiar, flat cell-shape optimizes the uptake of nutrients and oxygen and its intracellular gas vesicles help to maintain a horizontal orientation to capture light (Table 5). In freshwater habitats dominance of algal blooms by G. semen has been attributed in part to a high photosynthetic rate that results from a combination of its high-efficiency chlorophyll a and a highly efficient chloroplast arrangement (Table 5).

18In open habitats that are nutritionally dynamic and/or complex (Table S1) metabolic versatility in nutrient utilization can enhance the competitive ability of microbes (for examples see Table 5). Pseudomonas putida and related species are remarkable in their range of nutritional strategies (Table 5; Timmis, ): they are able to catabolize an indeterminate number of hydrocarbons (e.g. decanoate, toluene) and other organic molecules (e.g. amino acids, and organic acids such as acetic, citric and lactic acid) for use as carbon and energy sources; amino acids, dipeptides, ammonium chloride, urea, ammonium nitrate, and other substances as nitrogen sources; amino acids, organic acids, sodium sulfite, thiouracil, agmatine sulfate, etc. as sulfur sources; as well as accumulating diverse substances as intracellular reserves (Chakrabarty and Roy,; Daniels et al.,; Table 5) enabling a switch to oligotrophic growth at low nutrient concentration (Table 5; Timmis, ). In addition, P. putida and closely related species have evolved a complex, cAMP-independent catabolite repression system which incorporates five different signals and enables an ordered assimilation of carbon, nitrogen and sulfur substrates from the most to least energetically favourable (Daniels et al., ). This may contribute to the ability of many pseudomonads to sustain vigorous growth in nutritionally complex habitats. Pseudomonads, and closely related bacteria such as Acinetobacter, are not only environmentally ubiquitous but can dominate microbial communities in numerous types of open habitat including the plant phyllosphere and rhizosphere, bioaerosols, oil sands, and other hydrocarbon-containing environments (see Table S1; Ogino et al.,; Röling et al.,; Louvel et al., ). Pseudomonas species are able to enhance the availability of hydrophobic substrates by secreting biosurfactants and, at the same time, tolerate the stress induced by the latter (see below). Despite their copiotrophic phenotype, pseudomonads utilize a number of strategies to maintain growth and metabolism under phosphate-, iron- or nitrogen-depleted conditions (Table 5), can synthesize glutamate via glutamate dehydrogenase rather than glutamate synthase (thereby consuming 20% less ATP; Syn et al., ), and have even been observed growing in distilled water (Favero et al.,; Hirsch, ). Specific enzymes of Pseudomonas aeruginosa are catalytically active even when cofactor nutrients are scarce, and some strains have a manganese-dependent superoxide dismutase which does not require iron and is upregulated at low iron concentrations (Table 5).

19Weeds such as lactic acid bacteria and S. cerevisiae that lack saprotrophic capabilities can dominate communities in habitats with high nutrient concentrations (Tables S1 and5); they possess high-affinity transport proteins that enable rapid and efficient uptake of substrate molecules to support their vigorous growth phenotypes (see Table 5). Cells of S. cerevisiae are not only highly efficient at storing carbohydrates (combined trehalose and glycogen may reach 25% dry weight; Aranda et al.,; Guillou et al., ), but they can also accumulate high concentrations of arginine and polyphosphate and have adaptations to retain activity under low-nitrogen conditions (Table 5). Plant weeds that excel in open habitats have distinct genetic properties; they are often of hybrid origin and/or polyploid, traits that give rise to increased growth rates and stress tolerance, and have specific genes that confer their vigorous phenotype (Anderson,; Hill,; Schnitzler and Bailey,; Bakker et al., ). There is also evidence that the multiple copies of genomic material found in vigorous microbes that enhanced vigour have arisen via hybridization and/or increased ploidy levels in bacterial weed species, as well as Pichia and Saccharomyces (Table 5; Cox, ). A recent study by Timberlake and colleagues reported vigorous growth for the majority of F1 hybrids produced by crossing 16 wild-type S. cerevisiae strains (although hybridization and/or polyploidy may not always be advantageous; see Table 5). Many microbial weed species are phenotypically variable (like their plant counterparts; Table 1; Hill, ) and may form part of a species complex due to polyploidization and hybridization (e.g. Acinetobacter, Pseudomonas, Mycobacterium, Saccharomyces sensu stricto; Table S1; Rainieri et al.,; Todd et al.,; Ballerstedt et al.,; Parkinson et al.,; Sicard and Legras, ); such factors may contribute to the vigour and weediness of such species.

20High-Mr macromolecules are the primary microbial substrates available in many habitats: e.g. hydrocarbons (in bioaerosols, oil-containing environments, and the rhizosphere), and polysaccharides (within or derived from plant necromass such as cellulose, lignin and humic substances; see Table S1). In order to out-compete other species in such habitats, microbes must utilize these macromolecular substrates that typically have a low bioavailability, require specialist enzymes to degrade, can be toxic, and/or are energy-expensive to catabolize. Facultatively saprotrophic microbes such as Aspergillus, Pichia, Rhodotorula and Acinetobacter species are able to access and catabolize recalcitrant polysaccharides; some weed species can produce exceptional amounts, or high-affinity versions, of inducible saprotrophic enzymes, such as xylanases (Table 5). Several saprotrophic enzymes produced by Aspergillus species (that can dominate physicochemically diverse habitats; Table S1) can retain activity over a wide range of environmental stresses (Hong et al., ); and Aspergillus, and Rhodotorula spp. are able to utilize a broad range of nitrogen substrates thereby avoiding the need for de novo synthesis (Table 5). Whereas nutritionally complex habitats can select for metabolic versatility (see below) and thereby favour the growth of a great number of generalist species, only a minute fraction of such microbes are able to dominate what were (initially) phylogenetically diverse microbial communities (Table S1).

21Grazing, predation and viral infections adversely impact the growth dynamics of and/or incur massive losses on microbial populations and so exert a powerful selective pressure, and this can be well illustrated by the ecologies of many planktonic species in aquatic habitats (Matz et al.,; Jüttner et al.,; Berdjeb et al.,; Thomas et al.,; Yang and Kong, ). The competitive ability of some aquatic bacteria and eukaryotes (both marine and freshwater species) is associated with their ability to resist or tolerate virus infection (see Table 6). Species with a halophilic growth phenotype, especially those which have high growth rates in salt-saturated environments such as S. ruber and H. walsbyi minimize losses to predators because these salt concentrations are hostile to protozoa due to their low water activity, high ionic strength, and/or (for high-MgCl2 and high-CaCl2 brines) high chaotropicity (Table 6; Hallsworth et al., ). Gonyostomum semen has evolved vertical migration patterns through the water column that are out of phase with those of grazing species and thereby minimizes losses (Table 6). Other weeds, including P. aeruginosa and M. aeruginosa, are capable of forming multicellular structures – micrcolonies – that are sufficiently large to reduce losses by many species of grazers and predators (Table 6). Species such as M. aeruginosa accumulate toxic metabolites, and M. aeruginosa and Aspergillus spp. are known to synthesize secondary metabolites that repel to grazing plankton and arthropods respectively (Table 6).

22A number of agricultural (plant) weeds are able to dominate their habitats due largely to the production of phytotoxic inhibitors that can be exuded from leaves, roots and plant necromass and which inhibit the germination and/or growth of other plant species (Hill,; Xuan et al.,; Alsaadawi and Salih,; Chou,; Meksawat and Pornprom,; Inderjit et al., ). It is likely that most microbial weed species also secure their competitive advantage – in part at least – via the deployment of antimicrobial substances. Assuming that the examples listed in Table S1 are representative of the microbial biosphere then the proportion of habitats dominated by eukaryotic species is approximately 40%. If a short generation time was sufficient to facilitate habitat domination then prokaryotic species would populate almost all these habitats. The fact that species of algae, fungi and yeast are also able to do so underscores the importance of factors other than generation time in the biology of habitat dominance. Saccharomyces cerevisiae provides an illustration of how one weed species combines the synthesis of a potent antimicrobial, energy generation, and coordinated synthesis of stress protectants in a single process, i.e. aerobic production of the chaotropic alcohol, ethanol (see above; Table 6). Ethanol can be produced and secreted at concentrations > 4 M that cause a reduction of water activity (to 0.896) and exert an exceptionally high chaotropic activity (see above) sufficient to prevent the growth or metabolism of any living system (Hallsworth,; Hallsworth and Nomura,; Hallsworth et al., ); S. cerevisiae simultaneously produces glycerol (which can reduce ethanol stress in yeast and fungi; Hallsworth,; Hallsworth et al., ) during ethanol fermentation and is metabolically wired to synthesize high concentrations of the protectant trehalose at the end of its growth cycle when ethanol concentration is highest (see Table 6).

23We believe that the bulk production and secretion of chaotropic solutes and organic acids (that can reach molar concentrations) is unique to microbial weed species (Tables 1 and 2). Whereas chaotropic substances can promote growth and expand the biotic windows of microbes under specific conditions (Hallsworth and Magan,; Williams and Hallsworth,; Bhaganna et al.,; Chin et al., ), in other circumstances chaotropicity can be highly inhibitory or even lethal (Hallsworth,; Hallsworth et al.,; Duda et al.,; Bhaganna et al., ). For plant weeds it is the early stages of habitat colonization that are key to their success (Hill, ), and is may be that the efficient synthesis of antimicrobials is frequently as important as much as the type of substance produced (Hallsworth,; Pretorius,; Eshkol et al.,; Fialho et al., ). Unlike plant weeds, where phytotoxic inhibitors tend to have the greatest impact on neighbouring plants, microbes can also produce volatile organic compounds (VOCs) that inhibit the growth of both proximal and distal cells via their dispersion in both aqueous and gaseous milieu (Table 6).

24Volatile organic compounds – including aldehydes, furones, terpenes and many alcohols – can be powerful inhibitors of microbial metabolism and growth (Table 6; Jorge and Livingston,; Passoth et al.,; Minerdi et al.,; Fialho et al.,; Corcuff et al., ). Despite their volatility they are to some degree also water-soluble, and are sufficiently inhibitory to prevent metabolic activity and growth, even in aqueous solution at subsaturated solute-concentrations (Bhaganna et al., ). VOCs with a log Poctanol-water < 1.95 typically partition into the aqueous phase of cellular macromolecules and can act as potent chaotropic stressors (Table 6; Hallsworth et al.,; Bhaganna et al.,; Cray et al., ). Those stressors with a log P of > 1.95 preferentially partition into the hydrophobic domains of membranes and other macromolecular systems, and thereby act as hydrophobic stressors that induce a distinct type of chaotropicity-mediated water stress (Bhaganna et al., ). We believe that the primary ecophysiological value of VOCs for microbial cells pertains to competition, species succession and (for weed species) habitat dominance. Saccharomyces cerevisiae synthesizes both hydrophobic and chaotropic volatiles that have antimicrobial activities, including ethyl octanoate and isoamyl acetate, and ethyl acetate and 2-phenylethanol (respectively, see Table 6; Fialho et al., ). Ethanol and 2-phenylethanol are synergistic in their antimicrobial activity (Ingram and Buttke,; Seward et al., ), and this is consistent with their common chaotropicity-mediated mode-of-action. The more potent chaotrope of the two (when compared on a molar basis) is 2-phenylethanol which prevents growth of microbes in the range 10–40 mM (Berrah and Konetzka,; Eshkol et al., ), values consistent with a chaotropic mode-of-action for a stressor with a log P of 1.36 (see Bhaganna et al., ). Saccharomyces cerevisiae (like P. anomala, Acinetobacter and lactic acid bacteria) also inhibits the growth of competing species by acidifying the environment which it achieves via the production of a number of organic acids (Table 6; Kotyk et al.,; Lowe and Arendt,; Gulati et al., ); it also secretes peptides with fungicidal and fungistatic activities (Albergaria et al., ); and some strains contain inheritable virus-like particles containing genes that code for proteins inhibitory to other strains of the same species (Pretorius, ). Not only does S. cerevisiae employ multiple types of antimicrobial substance that act in concert, it is also has a correspondingly wide range of stressor-protection measures that minimize metabolic inhibition by antimicrobial stressors (those synthesized by either S. cerevisiae or other species), including efflux pumps (Pretorius, ), and highly effective compatible-solute strategies (see above), protein-stabilization proteins and adaptations to acid stress (Table 6) and is therefore highly tolerant towards chaotropic and hydrophobic stressors (Fig. 2; Tables 4 and 6). Saccharomyces cerevisiae acid tolerance (as well as that of lactic acid bacteria) is conferred by an array of mechanisms (Table 3) that collectively contribute to the weed phenotype by removing the hydrogen ions and/or by promoting the refolding of partially denatured biomacromolecules.

25Pichia anomala utilizes an array of antimicrobials that have synergistic effects as inhibitors and collectively target a wide array of taxa (including fungi, other yeasts, bacteria and viruses; Walker, ): chaotropic stressors such as ethanol and ethyl acetate; hydrophobic stressors such as isoamyl acetate; biosurfactants (see below); organic acids; an exo-β-1,3-glucanase known to degrade glucans in fungal cell walls; and diverse toxins that have specific modes-of-action (see Table 6; Passoth et al.,; Walker et al., ). A semi-quantitative analysis of the antifungal activities of P. anomala suggests that inhibition results primarily from a combination of (in order of importance): killer toxins, hydrolytic enzymes and volatile substances (Table 6), as well as more minor factors such as nutrient competition and substrate acidification (Walker, ). Rhodotorula mucilaginosa produces an array of volatile chaotropic and hydrophobic stressors as well as killer toxins (Table 6). Many fungi also produce mycotoxins; for example Aspergillus ochraceus growing on maize grain can produce ochratoxins at up to 1.4 mg g−1 (Magan et al., ). Indeed a number of Aspergillus species are notorious for the potent activity of their ochratoxins against other fungal strains and as well as bacteria (Table 6).

26Like S. cerevisiae, some other microbial species are able to produce moderately chaotropic antimicrobials in bulk quantities: Clostridium acetobutylicum produces high concentrations of butanol, ethanol and acetone in anaerobic habitats, and Zymomonas mobilis produces high concentrations of ethanol (Tables S1 and6). Butanol is a particularly potent chaotrope that is highly inhibitory at millimolar concentrations (Bhaganna et al.,; Ezeji et al.,; Cray et al., ). We suspect that Clostridium spp. that can dominate chaotropic environments such as ammonia-rich animal slurries (Table S1) have an unusually high resistance to the net chaotropicity of the ammonia, ethanol, butanol, acetone and other chaotropic substances in their habitat (a hypothesis that has not yet been investigated to our knowledge; Williams and Hallsworth,; Cray et al., ). The chaotropicity of urea and ammonia is greater than that of ethanol when compared at equivalent molar concentrations (Hallsworth et al.,; Williams and Hallsworth, ) and there is evidence that some bacteria that secrete these compounds, including Clostridium aminophilum and Pseudomonas stutzeri, benefit from chaotropicity-induced inhibition of their competitors (Table 6). There is no absolute resistance to the inhibitory/lethal activities of chaotropic and hydrophobic stressors (Sikkema et al.,; Hallsworth,; Hallsworth et al.,; Duda et al.,; Bhaganna et al.,; Bell et al., ) so the production of such antimicrobials coupled with reasonably effective self-protection mechanisms (see Tables S1 and6) can sometimes be the ultimate means to achieve community dominance (see also Table S1).

27Pseudomonas putida can generate and/or secrete diverse antimicrobial substances including catabolites produced from degradation of macromolecular substrates, VOCs and biosurfactants (Table 6). Biosurfactants that solubilize hydrocarbons and other hydrophobic substrates can also be highly inhibitory to other microbial species. Studies of Pseudomonas rhamnolipids suggest a key role in competitive ability (Wecke et al., ); surfactants not only disorder plasma membranes and solubilize lipids, but can be chaotropic even for macromolecules that lack hydrophobic domains (Table 2; Cray et al., ). The membrane-permeabilizing activities of rhamnolipids are particularly detrimental to Gram-positive bacteria, and are lethal to Phytophthora zoospores (Kruijt et al.,, Wecke et al., ). Bacteriocins produced by pseudomonads, like those of lactic acid bacteria, modify cellular membranes increasing permeability, causing leakage, disrupting transport processes and causing a dissipation of proton-motive force (Table 6). Catabolites such as phenol, catechol, vanillin, biphenyl, and sodium benzoate that are produced from the degradation of high-Mr hydrocarbons have inhibitory activity as chaotropic and hydrophobic stressors (Table 6; Hallsworth et al.,; Bhaganna et al., ). Pseudomonas putida and other pseudomonads produce a wide variety of VOCs that collectively impact microbial competitors (Table 6). As outlined above, P. putida has multiple layers of defence against the potential stressful impact of solvent, chaotropic, and hydrophobic stressors via a versatile compatible solute metabolism (e.g. trehalose; Park et al.,; Bhaganna et al., ), protein-stabilization proteins, and production of extracellular polymeric substances etc. (Tables 3 and 6). In addition, and arguably the most important feature for stressor tolerance, P. putida cells are equipped with efflux pumps (for example the plasmid-encoded TtGHI) that are highly effective at expulsion of hydrocarbons such as toluene as well as many other stressors and toxins (Ramos et al.,; Fillet et al., ).

28Whereas the aquatic habitats of planktonic species such as D. salina, G. semen and M. aeruginosa may serve to dilute secreted antimicrobials, there is evidence that VOCs produced by D. salina, M. aeruginosa, and other aquatic species (including compounds such as β-cyclocitral and dichloromethane) are inhibitory to competing species (Table 6). Gonyostomum semen is able to lyse the cells of competing algal species on contact although the mechanism by which it does so has yet to be resolved (Table 6); and M. aeruginosa synthesizes a diverse range of volatile antimicrobials including phenazines and phenazine derivatives (Table 6; Lifshits and Carmeli, ). Lactic acid bacteria, in addition to bacteriocins, produce significant quantities of organic acids and secrete a vast array of inhibitory VOCs (Table 6). The analysis of volatiles produced, primarily by L. rhamnosus, during the production of a ewe's-milk cheese (Table S1) gives an insight into the complexity of the microbial warefare that takes place in open habitats: 57 compounds were detected including terpenes, alcohols, ketones and esters (Randazzo et al., ) Although it is plausible that some of these substances exert specific toxic effects, all of them have the properties of either chao- or hydrophobic stressors in microbial cells (Table 6; Bhaganna et al., ), and their roles in habitat dominance has rarely received attention.

29The concept of an open habitat is a fundamental, well-established principle in the fields of plant and animal ecology. For microorganisms, open habitats can be defined according to the diversity, interactions and community succession of their inhabitants in contrast to other types of microbial habitat that are defined by physicochemical characteristics, substrate type or nutrient concentration (Table 7). Hydrocarbons are the primary carbon substrate in approximately one-third of the open habitats listed in Table S1, and are generally derived from dense, non-aqueous phase liquids (e.g. oil) or plant metabolites secreted into the rhizosphere, phyllosphere or atmosphere (bioaerosols). A distinguishing feature of hydrocarbon-based systems is that they can remain perpetually open because, as dissolved hydrocarbons are assimilated, the substrate reservoir may be continually replenished by molecules from the oil entering the aqueous phase or (for the rhizosphere and phyllosphere) because the plant continues to produce and secrete hydrocarbons and other organics (Nunes et al.,; Kazda and Falkinham III,; McCammick et al.,; Hunter et al.,; Kachalkin and Yurkov, ). These habitats are commonly dominated by species such as Acinetobacter johnsonii, Alkanivorax borkumensis, Pantoea ananatis and P. putida. Whereas these organisms – all members of the gammaproteobacteria – may share many molecular and ecophysiological characteristics (see Tables 3) in most cases it is P. putida that emerges as the most prevalent species (Table S1). This is a product of its metabolic versatility, exceptional tolerance to hydrocarbons and other solutes, and antimicrobial activities (Tables 5 and 6). Other weed species, however, have greater acid tolerance than the gammaproteobacteria: in the acidic surface film of the sphagnum-moss grey layer it is Mycobacterium (including Mycobacterium terrae, M. smegmatis and Mycobacterium sphagni) that emerges as a dominant genus; and in the green layer at lower pH (2–2.5), R. mucilaginosa has the competitive advantage (Table S1). Phyllosphere, rhizosphere and other habitats can also remain continuously open if they are replenished with organic substances from ions released from soil particles, extracellular polymeric substances and compatible solutes from microbial cells, root diffusates, animal wastes, diverse sources of necromass, etc.

30Habitats which facilitate weed emergence are typically not so extreme that there is a negligible microbial diversity or little capacity for community development/biomass formation; i.e. > 0.75 water activity, < 20–25 kJ kg−1 mole−1 chaotropic activity, < pH 11 or > −15°C (Table 7). Open habitats have available nutrients, electron acceptors etc and C: N ratios that favour microbial growth, and do not contain high levels of inhibitory substances such as heavy metals or toxic pollutants. They will therefore promote intense competition between species assuming that a diversity of microbial species is present (Tables S1 and7). Whereas high-sugar habitats with a water activity below 0.9 are too stressful for the vast majority of microbes, including S. cerevisiae, there is still a considerable diversity of xerotolerant and xerophilic species that are highly active between water activities of 0.84 and 0.9 (Pitt,; Brown, ). Similarly, crystallizer ponds or solar salterns are known as extreme environments and only a small fraction of microbial species can survive and grow at saturated NaCl. Nevertheless, it is the limited solubility of NaCl (and not the limitations of salt-adapted macromolecular and cellular systems) that determines the limit for microbial growth in high-NaCl habitats: a number of obligate halophiles grow optimally at 35% w/v NaCl (0.755 water activity) and different types of NaCl-saturated environment are biodiverse, highly competitive, biomass-rich microbial habitats (Antón et al.,; Daffonchio et al.,; Baati et al.,; Bardavid et al.,; Khemakhem et al., ). Salterns (and also algal mats) may under some conditions function as continually open habitats if nutrients are not limiting; D. salina for example can release sufficient glycerol into the system to satisfy the carbohydrate requirement of the wider community (Borowitzka,; Bardavid et al., ).

31Open habitats favour microbes with shorter generation-times and relatively vigorous growth-phenotypes and in this way may drive the evolution of faster-growing and more stress-tolerant species (as well as those with effective antimicrobial strategies; Tables 6 and 7). That the ecology and evolution of plant weeds are intimately and inextricably linked with open habitats has been established for some time (Anderson, ); in contrast there is little information about open habitats of microorganisms (see Table 1; Hallsworth, ). Open habitats can be spontaneously created (e.g. due to removal of microbial biomass by predators and grazers; McArthur, ), dynamic (e.g. due to desiccation–rehydration cycles or nutrient limitation), and/or transient (Tables S1 and7). As is true for open habitats of plants (Anderson, ), open habitats of microbes can also become closed if they becomes water-constrained or otherwise resource-depleted; and/or the microbial community reaches stationary phase (Paul et al., ): and these changes may be accompanied by – or even a consequence of – domination by weed species. Environments can even progress to become sterile; for example those with high ethanol concentrations (Hallsworth,; Pretorius, ). However, a dualistic concept of open habitats on the one hand and closed habitats on the other would be simplistic; in reality there is a seemless continuum between the two extremes of fertile but uncolonized and hostile/uninhabitable environment. Habitats with a favourable water activity for most bacteria (≥ 0.94) and high concentrations of carbon and nitrogen substrates such as milk, cheese and crushed peanuts (Table S1) typically progress to a closed condition (and are dominated by lactic acid bacteria), as do most high-sugar habitats (Table S1). A number of the open habitats listed in Table S1 that are resource-rich, and stressful, temporally or spatially heterogenous, and/or require saprotrophic nutrition were dominated by Pichia (e.g. moist barley grains; salted fermenting olives) or Aspergillus species (e.g. decomposing leaf litter, sugarcane juice). The stress biology, energy-generating capabilities and antimicrobial activities of these species undoubtedly contribute to their success (Tables 3 and 6).

32Microorganisms have been previously categorized based on the way in which their phenotype impacts ecological behaviour: as autotrophs and heterotrophs; generalists and specialists; r- and K-strategists, aerobes and anaerobes; copiotrophs and oligotrophs; fast and slow growers; and extremophiles and mesophiles (see Table 4 and S2). The definition of microbial weeds is qualitatively distinct from that of other microbial groups (see Table S2): only weeds are characterized by their ability to dominate communities and the associated/underlying biology (Tables 2) and it is only weeds that are linked via their ecology and evolution with open habitats (Tables 1, S1, and S2). The biology and ecology of microbial weed species cuts across established groupings of microorganisms (i.e. the former does not represent a parallel category; see Table S2). Some microbes have a considerable number of weed traits but only rarely emerge as dominant members of communities (e.g. Pseudoxylaria spp., E. coli and M. smegmatis; see Tables S1 and5 and 6). Such species serve as a reminder that weeds and non-weeds represent two extremes of an otherwise continuous scale. An insightful study of Termitomyces ecology, for example, discusses the biology of Pseudoxylaria; a fungus that is present in Termitomyces habitats but is typically inactive and/or present at negligible cell densities (Visser et al., ). Pseudoxylaria could be ecologically disadvantaged if present in greater numbers as termites, which can detect VOCs produced during interactions between Pseudoxylaria and Termitomyces, remove the unwanted fungus from their Termitomyces cultures. The extant Pseudoxylaria strains thereby appear to have been selected for/have evolved a low competitive ability (Visser et al., ). Nevertheless Pseudoxylaria can occasionally emerge to dominate the substrate (Visser et al., ), a fertile open habitat consisting of decomposing plant material (Table S1). Non-weed species make up a loose affiliation of species that are only linked by their poor ability to dominate communities in open habitats and may not share any specific metabolic or phenotypic traits (Table S2). We propose that this ‘dustbin’ group includes Synodropsis spp., Polypaecilum pisce, Metschnikowia orientalis, Caulobacter crescentus and Salmonella species (Table S2). Several ecophysiological classification systems that are based on microbial growth-phenotype and/or substrate utilization (Table S2). Microbial generalists can occupy a wide range of ecological niches, and typically achieve this via the ability to utilize a wide range of nutrients and substrates (Table S2). Conversely microbial specialists, such as S. cerevisiae, H. werneckii and many basidiomycetes have specific nutritional and/or physicochemical requirements (de Fine Licht et al.,; Kashangura et al., ). Obligate extremophiles commonly occupy, and are adapted to grow optimally in, niches that are hostile to the majority of microorganisms (Table S2). There have been relatively few studies (and is consequently inadequate terminology) to properly describe microbes that are extremo-intolerant such as xero-intolerant species (see Table 4), with the exception of mesophilic species that function optimally at non-extreme temperatures (though the term mesophiles can be used in a general sense to refer to non-extremophiles: Table S2; Gostinčar et al., ). Non-extremophilic microbes grow optimally in physicochemical conditions which favour metabolic activity and growth of the majority of microbial species, and this grouping includes both weed and non-weed species (Table S2). While fast-growing microbes have short doubling times, the vast majority of these species do not have weed-like capabilities and are unable to out-grow their competitors (Tables 4 and S2). It may be that relatively few oligotrophic microbes or K-strategists are weed species, although some mycobacteria do have a weed phenotype (Tables S1,5 and 6). Pseudomonas putida is generally considered to be a model r-strategist (e.g. Margesin et al., ) yet P. putida has an extraordinary competitive ability (see Tables S1 and6), and may not be the best example of an r-strategist (the latter are characterized by a weak competitive ability; Table S2). By contrast P. putida appears to be an exceptional example of a microbial weed both in terms of its cellular biology and its ability to dominate diverse types of open habitat.

33It is irrefutable that a small minority of microbial species recurrently appear as the dominant members of microbial communities; and we suggest here that these microbes have shared phenotypic traits. This implies that open-habitat ecology has impacted the evolutionary trajectories of these microbes, and that the activities of weeds determine microbial diversity in many localities within the biosphere. Whereas microbial weed species are not always useful to humankind (see Table 1), they make up a substantial portion of the world's biotechnology sector. Saccharomyces cerevisiae supports global industries in fermented products, biofuel, biocides (ethanol is also an important disinfectant; McDonnell and Russell, ), and other white biotechnologies; P. anomala produces a substantial catalogue of biotechnologically useful substances and is employed in production of foodstuffs (see Walker, ); lactic acid bacteria form the basis of food- and drinks-production processes where the antimicrobial volatiles and organic acids that they secrete act as flavour compounds and natural preservatives, and are used as probiotics, and for the production of fine chemicals (Rose,; Steinkraus,; Molly et al.,; Nomura et al.,; Tiwari et al.,; Randazzo et al.,; Bron et al., ); P. putida is used for the commercial production of bulk and fine chemicals, industrial biocatalysis, and as the basis of many other industrial and environmental biotechnologies (Kruijt et al.,; Puchałka et al.,; Hassan et al.,; Poblete-Castro et al., ); a number of weed species, including Aspergillus spp., P. putida and Clostridium spp. play primary roles in the treatment or decomposition of plant matter, oil and hydrocarbons, xenobiotics in polluted soils, sludge and slurry treatments, and other organic wastes (Tables S2 and4; Narihiro and Sekiguchi,; Timmis, ); and Aspergillus species are used for production of foods (Rose,; Tamang, ), fine chemicals (e.g. citric acid, secondary metabolites) and extracellular enzymes (e.g. amylase, cellulase, pectinase and protease), for industrial biocatalysis, and have potential for bioremediation and biosorption applications (Ward et al., ). It is the metabolic activities of substances that suppress potential competitors which make S. cerevisiae, Rhodotorula spp., P. anomala, P. putida, lactic acid bacteria and other weed species invaluable as agents of biological control, for preventing spoilage of drinks, foodstuffs and animal feeds (see Calvente et al.,; Kruijt et al.,; Hassan et al.,; Olstorpe and Passoth,; Walker, ).

34Microbial weeds are also used as model systems for research, yet key aspects of their biology remain enigmatic. Many plant weeds have exceptional reproduction and dispersal systems (Table 1) and it remains unclear whether microbial weed species produce more propagules, have superior dispersal mechanisms, or evolved propagules with exceptional longevity, and/or the ability to germinate over a wider range of conditions than their non-weed comparators. Could it be that, like plant weeds, the competitive ability of microbial weeds is enhanced by an abnormally high phenotypic plasticity and intra-specific variability (see Table 1)? Out of the world's plant flora it has been estimated that only several hundred plant species are weeds (Hill, ); what percentage of microbes might exhibit weed phenotypes and behaviour? Is there evidence preserved in rocks, sediments, peat, ice, or the hypersaline fluid inclusions of salt crystals that can shed light on the evolutionary trajectories of microbial weed species? Is there an ideal genome size for prokaryotic and eukaryotic weed species? What are the minimum/essential characteristics required to enable a microorganism to dominate a specific habitat; can we design and manufacture a microbial weed via a synthetic biology approach? Will hitherto uninvestigated microbial weeds prove to be rich sources of antimicrobial compounds for novel biotechnological and clinical applications? Can microbial weed ecology shed light on wound microbiology, lead to the prevention of the microbial colonization of prosthetic devices, or minimize the emergence of opportunistic pathogens? Could knowledge-based interventions in weed ecology enhance our ability to manipulate and manage microbes at various levels of food-production and food-spoilage, or lead to better management of environments that harbor potentially dangerous species?

35Crop plants such as sunflowers, potatoes, wheat and barley are known to have weedy ancestors (Anderson, ) and it is thought that the evolution of both plant weeds and crop plants has been driven by anthropogenically opened habitats. We believe that open (microbial) habitats also select for the phenotypes, and therefore act as a potent driving force that determines the evolutionary trajectories, of microbial weeds and their communities: open-habitat ecology may therefore be worthy of recognition as a distinct scientific field that spans all organismal biology including microbiology. There is a maxim that everything is everywhere but that the environment selects; this implies that microbial species are everywhere on Earth but that the local environment determines which are able to grow (Baas Becking,; de Wit and Bouvier, ). While not necessarily untrue, this idea implies a level of passivity on the part of the microbial cell. Yet microorganisms are inherently variable and dynamic systems with considerable genetic dexterity and phenotypic plasticity (able to both respond and adapt). Baas Becking acknowledged that cells are able to modify their extracellular environment, but microbes are also proactive in their manipulation of each other. It may be that microbial weeds are the most accomplished examples of this.