Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review

1Prokaryotes, the unseen majority sustaining life on Earth, are involved in a multitude of interactions and biogeochemical processes having global ecological relevance, including decomposition, mineralization, storage, and release of nutrients. The number of prokaryotes present in a gram of soil can be between 106 and 109 cells. It is apparent from the above data that there is an abundant density of bacteria in the soil, however, the discrepancy is that only less than 1% bacteria from natural environments, including soil, could be cultivated by using conventional culturing techniques. A large segment of the microbial community gets consistently overlooked during routine microscopic analysis, indicating them to be novel and hitherto unrecognized with ambiguous physiology and growth requirements. A rational investigation stemming from the recognition of this discrepancy is the identification of these refractive bacteria which escape conventional enrichment and isolation procedures. In this direction, the 16S rRNA gene, the gold standard for phylogenetic analysis, proves to be a useful tool for studying the evolution-based taxonomy of microbial communities from various econiches. The rare biosphere comprises of several identified novel bacterial lineages, which appear to be profoundly branching within the bacterial tree and remain unaffiliated with any known bacterial phyla and are termed as candidate phylum (or candidate division).

2Molecular studies in the soil revealed the presence of unseen, hidden, recalcitrant bacteria referred to as difficult-to-culture, hitherto-unculturable, or yet-to-be cultivated bacteria. In contrast to standard fast-growing bacteria, these underexplored bacterial groups remain elusive to conventional microbiological cultivation techniques, mostly because their optimized growth conditions are still underexplored. The proportion of such bacteria exceeds far more than that of the culturable ones. Among them, Acidobacteria constitutes the most abundant phylum whose members dominate soil bacterial communities. Data from 16S rRNA gene inventories signify the vastness and breadth of the phylum with genetic and metabolic diversity. Study of these hitherto-unculturable constituents of soil microbial population through culture-dependent and -independent approaches revealed the essence of their bioactivity and their ecological functions in plant-soil ecosystems. The underexplored phylum Acidobacteria thus provides an enthralling and seamless source of biological diversity, offering new avenues for exploitation. Henceforth, the most recent advances mining the difficult-to-culture soil acidobacterial diversity for biotechnological advances and comprehensive understanding of the genetic diversity and ecophysiological profiles of Acidobacteria in the plant-soil econiche has been scrupulously presented in this review.

3Acidobacteria represents an enigmatic phylum with its members copiously distributed in different ecosystems. Acidobacteria is ubiquitous in diverse terrestrial environments ranging from tundra soils to desert soils, from peatland soils and sediments to grasslands, forests, and agricultural lands and constitute about 5–70% of the soil microbial populace. The members are recalcitrant, rendering this phylum to be feebly understood. The recalcitrance of most Acidobacteria members to grow on conventional growth media can be attributed to their oligotrophic nature or ecological K-strategy. Thus, the use of low nutrient media, modified incubation conditions including elevated CO2, low pH, prolonged incubation periods, and supplementing growth media with amendments like antioxidants, rhizosphere extracts, etc., have led to the isolation of several acidobacterial species.

4Based on the analysis of major 16S rRNA gene sequence clades, the phylum Acidobacteria is phylogenetically classified into 26 subdivisions. Among these, only seven subdivisions (namely the subdivisions 1, 3, 4, 6, 8, 10, and 23) are represented by taxonomically described members. Although more than 12,000 distinct phylotypes and more than 6,500 species-level operational taxonomic units have been reported so far for this predominant soil bacterial group, yet it is described by only 56 cultivable species belonging to 28 genera. All cultured Acidobacteria members are Gram-negative, non-spore formers, and exhibit an oligotrophic mode of nutrition. Most of the members are acidophilic chemoheterotrophs growing aerobically under mesophilic conditions. To study this phylum, culture-independent approaches have been more successful rather than culture-dependent approaches. Genomic studies provided insights into the genetic make-over of about ten acidobacterial genomes only. However, owing to the difficulty in cultivating its members, the in-depth ecological purview of this enigmatic phylum has remained evasive. Since information regarding global distribution patterns and apparent ecological roles of Acidobacteria is inadequate, microbial ecologists are deeply engaged to unfurl this obscure phylum.

5Acidobacteria phylogenetic diversity, richness, abundance, ubiquity, especially in soil ecosystems, pin down their roles in various biogeochemical cycles and broad metabolic versatility. Although their presence and abundance are confirmed through culture-independent studies but their ecological functions, interrelations with environmental parameters and interactions with other soil microbial communities remain obscure. Significant variations have been encountered during isolation of Acidobacteria strains belonging to different lineages and getting cultivated under specific sets of physicochemical conditions or nearly a narrow range of conditions. This suggests the use of various strategies for the successful recovery of ecologically different Acidobacteria groups.

6Acidobacteria diversity and dominance is quite pronounced along with high overall ecological and phylogenetic diversity in contrast to its low cultivation success due to radically different culture laboratory conditions. Although nine different bacterial phyla viz., Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi, Planctomycetes, Gemmatimonadetes, and Firmicutes are known to dominate in soil, the phylum Acidobacteria represents the most predominant not-yet-cultured, or difficult-to-culture group of bacteria, occupying a significant fraction of the soil microbial community. Henceforth, the determination of their ecophysiological roles becomes quite imperative to understand their functional status in complex bacterial communities. Thus, the ecological roles of Acidobacteria have been studied by analyzing the genetic components obtained by complete and/or draft whole-genome sequencing for culturable species and metagenome sequencing for unculturable species.

7Meta-microbiomic (16S rRNA gene-based) studies analyze only one specific gene and not the entire genomes of the community members. The 16S rRNA gene sequences, obtained from various environments by employing culture-dependent and culture-independent approaches, provide deeper insights into the species structure and taxonomic diversity of the phylum Acidobacteria. Studies focusing on 16S rRNA genes provide taxonomic status in any bacterial community, while metagenomics can provide both taxonomic and functional profiles of the microbiota. Metagenomic DNA extracted from the environment is often amplified using group or species-specific primers targeting 16S rRNA genes. Metagenomics has facilitated in an apt understanding of the diversity, abundance, genomic make-up, and ecological roles of acidobacterial members in various ecosystems. To obtain a complete community structure, 16S rRNA analyses and metagenomics are often used in conjunction (Figure 1).

8During recent years, the sequencing of collective community genomes employing metagenomics has led to a significant breakthrough in understanding the enigmatic phylum Acidobacteria. Subsequent advent and development of several next-generation sequencing (NGS) platforms further enhanced the metagenomic sequencing efficiencies. Metagenomic approaches, however, at few places fail to retrieve genome scaffolds of sizable length due to soil community complexity, intricacy, and absence of genomes. Recovering genomic information from the soil environment requires the use of large insert strategies. Metagenomic DNA being high in molecular weights requires meticulous isolation strategies along with novel cloning and screening methods to facilitate the recovery of large DNA fragments from difficult-to-culture bacterial genomes. Large genomic fragments might contain intact metabolic pathways. Acidobacterial genome fragments were successfully recovered from the environment by using a large metagenomic insert. Henceforth, such approaches provide important platforms for exploring the hidden biotechnological potential of hitherto uncultured bacteria leading to the discovery of novel organo-chemical compounds.

9Since the recovery of the first Acidobacteria member and subsequent advances in sequencing technologies has provided a platform to study individual Acidobacteria members at the genomic level. It is quite unfortunate that the number of thoroughly studied genomes of this important phylum is very few, despite their numerical abundance in many environments. Genomic studies have unveiled the hidden physiological and metabolic versatility of Acidobacteria members. Comprehensive studies targeting functional characteristics encoded in acidobacterial genomes may provide new vistas into ecological perspectives of phylum Acidobacteria. conducted detailed genomic studies for the first time, with three acidobacterial strains [two from subdivision 1 viz., Acidobacterium capsulatum and Candidatus Koribacter versatilis (strain Ellin 345) and one from subdivision 3 viz., Candidatus Solibacter usitatus (Ellin 6076)]. Further genomic profiling and comparative genomic studies provided more profound insights into the acidobacterial genome and ecophysiology.

10Insights into these genomes reveal large genome size (up to 10 Mbp) and a higher percentage of paralogous genes, which might endow the bacterial strains with potential ecological functions. In the same breath, Acidobacteria genomes also possess a comprehensive physiological set of genes that allows them to adapt to various ecological niches. An overview of the general genomic features of Acidobacteria members and their overall genetic and genomic make-up are respectively represented in Table 1 and Figure 2. Data available from published acidobacterial genome sequences reveal the presence of several genes involved in regulating carbon, nitrogen, and sulfur cycles, and those required for degrading different complex polysaccharides. All cultured Acidobacteria species are reported to produce exopolysaccharide (EPS); the presence of eps gene clusters in the genomes further supports this data. The acidobacterial genomes also contain a substantial proportion of genes encoding for various transporters, to tide over stress and starvation, and for the biosynthesis of cellulose, N-acyl-homoserine lactones, polyketides, siderophores, hopanoids, and mobile genetic elements.

11Each bacterium carries its enzyme machinery catalyzing the breakdown of diverse carbohydrates and nitrogen-containing compounds, which could be used as an identifying characteristic for differentiating varied bacterial species. Acidobacterial genomes possess genes encoding enzymes for the degradation of complex carbohydrate polymers viz., xylan, cellulose, hemicelluloses, pectin, starch, and chitin; amino acids, alcohols, and metabolic intermediates. In addition to these, gene modules for diverse carbohydrate breakdown, utilization, and biosynthesis within carbohydrate-active enzymes (CAZy) family are also present, spanning across 131 glycoside hydrolase (GH) families. Putative chitinases belonging to GH18 and GH19 family were also identified in the genomes of a few select Acidobacteria. Gene calling and annotation studies of Acidobacteria Group 1 Acidipila sp. strain EB88 genome indicated that it was rich in glycolytic enzymes and contained about 85 glycoside hydrolases in 48 families.

12The acidobacterial genomes are flexible and novel in their carbon metabolizing activity. Few select acidobacterial genomes exhibit anaplerotic CO2 fixation. Strikingly, homologs of phosphoenolpyruvate carboxylase and isocitrate dehydrogenase have also been detected across several Acidobacteria genomes. Studies suggest a crucial role of these genes for carbon metabolism in various nutritional pathways as well as a significant role in desiccation resistance, as evidenced by the Terriglobus saanensis genome profile. A significant contribution is made by acidobacterial enzyme machinery in regulating the carbon biogeochemical cycle. Since Acidobacteria are endowed with the potential to degrade polymeric carbonaceous complexes, they act as decomposers in soil and actively participate in the cycling of organic matter arising from plants, fungi, and insects.

13Acidobacteria is well equipped with genes catalyzing the metabolism of inorganic and organic sources of nitrogen. They can effectively reduce nitrate, nitrite, and possibly nitric oxide, as could be evidenced by genomic data, supporting their active participation in nitrogen nutrient circuits. Homolog candidate genes for nitrate reductase (nirA) have been identified in Ellin 345, Geobacter fermentans, and Terriglobus aquaticum, while those for nitrate transport (nrtABCD) have also been observed in certain acidobacterial strains. The presence of genes encoding dinitrogenase (nifD and nifK) and dinitrogenase reductase (nifH) have also been reported in one acidobacterial genome. However, experimental evidence regarding nitrogen fixation by Acidobacteria is missing. Insights into the core genomes provide a wealth of data revealing the presence of putative homologs encoding for extracellular peptidases, which play significant roles in soils by mobilizing ammonium and other intermediates of N-cycle. Serine endopeptidases are also found to be widely distributed in most Acidobacteria genomes, indicating their proteolytic activity in soil. Homologs for various extracellular metalloendopeptidases too span across select Acidobacteria genomes, facilitating them for N-uptake during mineral scarcity. Recent studies on the draft genome of Acidobacteria Group 1 Acidipila sp. strain EB88, isolated from forest soil, indicated that the genome lacked the genes required for organic acid uptake but was equipped with the genes essential for amino acid, ammonium, and nitrate uptake.

14Chloroacidobacterium thermophilium, a photoheterotrophic member of Acidobacteria subdivision 4, requires reduced sulfur for its growth. Draft metagenome-assembled genomes of Acidobacteria subdivisions 1 and 3 from peat soil revealed the presence of putative genes for dissimilatory sulfur metabolism (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP, aprBA, qmoABC, supP, hppA, sat) which function under anoxic conditions. The presence of dsrAB genes encoding dissimilatory (bi)sulfite reductase suggests the capacity of some Acidobacteria members to perform dissimilatory sulfate/sulfite reduction. Certain acidobacterial genomes also encode the dsrL gene, which is specific to the sulfur oxidation pathway. The presence of dsrL is unusual as it is generally found in sulfur oxidizers rather than in sulfate-reducing microorganisms. However, acidobacterial genomes lack any other genes involved in oxidative sulfur metabolism.

15Different acidobacterial strains harbor an array of genes encoding different ion channels, high-affinity ABC transporters, several other secretory porters, and transport proteins especially required for tiding on oligotrophic conditions. Genes encoding iron permease FTR1 and FTR2 family proteins and iron transporter genes viz., Mn2+ and Fe2+ transporters are also present in the Acidobacteria genome. The feoAB gene encoding a high-affinity ferrous iron transport protein is invariably present in acidobacterial genomes. The genome of Terriglobus saanensis (isolated from the Tundra region) contains abundant genes involved in carbohydrate metabolism and transport. Few Acidobacteria genomes also possess multiple copies of genes for siderophore transport viz., tonB, exbB, and exbD. In addition to these, pvuE (candidate gene for vibrioferrin transporter) and feoB (candidate gene for enterobactin transporter) are also found in some Acidobacteria genomes. Acidobacteria members also have genes for the amino acid-polyamine-organocation (APC) superfamily of transport proteins along with dicarboxylate/amino-acid: cation symporter family of secondary transport proteins.

16Acidobacterium capsulatum genome contains an operon with a complete set of genes required for cellulose biosynthesis. Bacterial cellulose is associated with an array of functions facilitating survival in the soil through biofilm formation, retaining moisture under conditions of stress, thus promoting aeration, contributing to soil aggregate formation. Acidobacteria possesses the remarkable capacity to synthesize cellulose, which would promote biofilms to get adhered easily to ferric iron-containing substrates producing biofilm-ferric iron-reducing “bioshrouds” in acidic environments. Cellulose biosynthesis via bcs operon has been reported in Terriglobus saanensis as evidenced through genome sequencing data. The genome of Acidipila sp. strain EB88 contained genes for biosynthesis and export of capsule and cellulose.

17Genomes of particular soil acidobacterial strains possess the potential to respire oxygen at atmospheric and microoxic levels due to the presence of affinity oxidases. Thus, such strains possess an extra selective advantage in the soil microenvironment, where low oxygen concentrations exist. The genome of Acidipila sp. strain EB88 contains a low-affinity group A heme-copper oxygen oxidase and five high-affinity cbb3 terminal oxidases that enables it to grow under both hypoxic and hyperoxic conditions. Few Acidobacteria strains possess hydrogen scavenging property due to the presence of nickel-iron [NiFe] hydrogenases. The occurrence of multiple structural genes (hhyS, hhyL, hhyE) and maturation genes (hypABCDEF) required for hydrogenase activity further supports acidobacterial hydrogen utilization.

18Acidobacteria genomes contain biosynthetic gene clusters that encode a vast repertoire of polyketide and non-ribosomal peptide synthases. Additionally, genes regulating the synthesis of diverse secondary metabolites and other natural compounds like siderophores, antifungals, antibiotics, antivirals, antitumor agents, and antinematodal agents have been reported in Acidobacteria genomes.

19Addiction modules encode various genes, including those required for plasmid maintenance, and has been documented in certain Acidobacteria. During stress or starvation, the addiction modules operate rapidly and inhibit DNA and protein synthesis. This mechanism of stress and starvation tolerance in Acidobacteria enables tiding over environmental oligotrophic nutritional conditions. The prokaryotic transcriptional regulator sigma factor is commonly utilized to control the expression of several gene sets in response to various stresses, including starvation, oxidative stress, heat stress, and exposure to heavy metals that enables the microorganisms to adapt to a stressful environment. The genomes of Candidatus Solibacter usitatus [Ellin 6076] and Candidatus Koribacter versatilis [Ellin 345] contain a vast repertoire of sigma E (σE) homologs (70 and 28 homologs, respectively) that are induced during starvation and other stress conditions.

20The presence of hydrogenases enables specific acidobacterial strains to consume atmospheric hydrogen, which could be a strategy to overcome starvation. Certain Acidobacteria members are equipped with the genes responsible for the dissimilatory reduction of nitrite to ammonia (nrfHA), which not only provides energy supply but also aids in the detoxification of nitrosative stress. A very recent study by reported that carotenoid production by Occallatibacter sp. (belonging to Acidobacteria subdivision 1) can confer tolerance to environmental oxidative stress. Thus, the production of carotenoids and related compounds may offer competitive benefits to soil Acidobacteria.

21Most Acidobacteria members prefer acidic conditions (3.0–6.5 pH) for their growth. Also, lower pH levels support a higher abundance of Acidobacteria. Microorganisms equipped with acid resistance (AR) systems are likely to survive in highly acidic conditions. Certain moderately acidophilic acidobacterial strains viz., A. capsulatum, Ellin 345 (K. versatilis), and Ellin 6076 (S. usitatus) contain candidate genes in the AR3 (arginine-dependent AR) system indicating the presence of an acid tolerance system. However, the strains lack the genes involved in other inducible AR systems, viz., AR1 (oxidative AR), AR2 (glutamate-dependent AR), and AR4 (lysine-dependent AR).

22Hopanoids are pentacyclic triterpenoid bacterial membrane lipids facilitating cell membrane permeability, especially during extreme environmental conditions. Genes related to hopanoid biosynthesis (shc gene) have been detected in Cadidatus “K. versatilis” belonging to subdivision 1 isolated from soil. The presence of C30 hopanoids and bacteriohopane polyols was reported in multiple Acidobacteria subdivisions, evident from the occurrence of respective biosynthesis genes (hpnA, hpnG, hpnH) in acidobacterial genomes.

23Genomic mining studies suggest that Acidobacteria belonging to subdivision 1 can encode EPS biosynthesis genes. Additionally, several cultured Acidobacteria species are known to secrete EPS. Gene prediction, along with functional annotation data, identifies a gene cluster encoding capsular polysaccharide in the genomes of three acidobacterial strains isolated from tundra soil. Granulicella mallensis genome possessed the epsH gene involved in exopolysaccharide synthesis.

24Quorum sensing molecules, like acyl-homoserine lactones (AHL), aid in coordinating gene expression in bacterial populations. Genomes of Acidobacteria contain a considerable fraction of genes encoding for biosynthesis of N-acyl homoserine lactones.

25Mobile genetic elements like transposons, bacteriophages, insertion sequence (IS) elements, and integrative and conjugative elements (ICEs) present in several Acidobacteria are known to confer shape and plasticity to the acidobacterial genome. These elements are speculated to mediate horizontal gene transfer, aid in the evolution and ecological success of Acidobacteria. A recent meta-study by identified 35 putative prophages across 19 acidobacterial genomes. Insertion sequence families encoding their mobility patterns also have been reported to be spanning across Acidobacteria genomes. Multiple genes encoding mobile elements, including transposases and IS elements, have been identified in the genome of Candidatus “Solibacter usitatus” Ellin 6076. Additionally, the genome also harbors genes encoding phage integrase family proteins and several other proteins containing a retroviral integrase catalytic region domain, catalyzing site-specific recombinations.

26Despite the recent progress in the field of acidobacterial ecology, there is still a paucity of complete information regarding their ecophysiological roles. Significant ecological functions have been reported in forest soil for Acidobacteria members. Acidobacteria members in plant-soil ecosystems play pivotal ecological roles, including modulation of biogeochemical cycles and influencing plant growth. The key findings from relevant studies on soil Acidobacteria, highlighting their salient genomic features and ecological roles, are summarized in Table 2. An overview of their ecological roles in the plant-soil ecosystems is diagrammatically represented in Figure 3 and is discussed below.

27A recent study by has reviewed and re-defined “keystone taxa” in microbial ecology. Microbial keystone taxa have been often ascribed as “ecosystem engineers” as they are the unequivocal drivers of microbial community structure and function in different ecosystems. Acidobacteria was reported to be one of the keystone bacterial taxa in soil associated with the decomposition of soil organic matter (SOM), implying their significance in carbon turnover. Computational inferences obtained from analyses of various terrestrial ecosystems and habitats indicate several subdivisions of phylum Acidobacteria represent the keystone taxa in grasslands (subdivision 4), forest or woodlands (subdivision 4), agricultural soils (subdivision 17), and plant-associated microbiota (subdivisions 1, 3, and 6). Speculations suggest that these microbial residents exert beneficial effects by selectively modulating the ecological processes of host ecosystems. These bacteria offer two crucial ecological services viz., SOM decomposition, and denitrification, thereby enhancing carbon stability. Successful manipulation of these soil dwellers might augment the key ecological process of soil carbon sequestration. Since Acidobacteria members have been identified as structural and functional keystones in plant-soil microbiomes and agroecosystems, they can be exploited to enhance crop performance and productivity.

28The gamut of living organisms invariably depends on the supply of essential elements such as oxygen, hydrogen, carbon, nitrogen, phosphorus, and sulfur for growth and survival. In any ecosystem, albeit biogeochemical cycles or nutrient cycles are regulated by the biotic and abiotic components of that system, but microorganisms play a key role in modulating them. The critical metabolic processes viz., nitrogen metabolism, carbon fixation, and methane metabolism, sulfur metabolism operating in microbes effectively control global biogeochemical cycling.

29Genomic studies highlight the carbohydrate utilization potential exhibited by Acidobacteria members. The presence of genes encoding enzymes for the degradation of complex carbohydrate polymers like cellulose, hemicellulose, chitin, xylan, and lignin derivatives signifies their active participation in the carbon circuit as decomposers in soil and cycling of organic matter derived from plants, fungi, and insects.

30Soil bacteria convert the inorganic nitrogen to organic compounds, which are, in turn, utilized by the plants and other microbes. In plant-soil ecosystems, Acidobacteria communities represent an important microbial guild, central in nitrogen cycling. Genomic evidence coerces the crucial role of Acidobacteria in N-cycling in soils. Specialized microorganisms metabolize diverse sulfur compounds via redox reactions and contribute to driving the global sulfur cycle. Acidobacteria genome harbors genes regulating sulfur metabolism that were found to be expressed in native peat soils and upregulated in diverse anoxic conditions, indicating their active role in modulation of the environmental sulfur cycle. reported that consortia of diverse sulfate-reducing microorganisms, including Acidobacteria members, drive the sulfur reduction in peatlands and Acidobacteria members (Holophaga) responded positively to sulfate stimulation in peat soil microcosms.

31Exopolysaccharides are bacterial polysaccharides synthesized extracellularly, which play a critical role in the soil matrix and aggregate formation. EPS plays a significant role in the development of mature biofilm by acting as bridges between cell surfaces. In the rhizosphere zone, EPS production by bacterial populations contributes toward nutrient and water uptake by plant roots through modification of the physicochemical properties of rhizosphere soil and aids in establishing interactions with the root appendages for successful plant-microbe interactions.

32Several cultured Acidobacteria species are known to secrete EPS. Genomic analyses indicate that Acidobacteria belonging to subdivision 1 can encode EPS biosynthesis genes. These EPSs might protect Acidobacteria, endowing them the ability to survive for prolonged periods in soil. Recently, the characterization of EPSs derived from two subdivisions 1 acidobacterial strain (Granulicella sp.) has indicated them to be possessing potential environmental, bioremediation, and biotechnological applications. These EPSs could be used as natural eco-friendly binders and formulants in the biofertilizer industry.

33Acidobacterial genome profiling validates the presence of cellulose synthesis genes along with related accessory proteins. Studies postulate several Acidobacteria members to possess the capability to establish biofilms, exhibit resistance toward desiccation, and aid in the formation of soil aggregates. However, physiological data confirming actual EPS production by Acidobacteria and validating their ecophysiological roles remains obscure.

34Plant root microbiome harbors beneficial microbes, which offer an eco-friendly alternative to improve plant growth and protect against phytopathogens. Plant growth promoting rhizobacteria (PGPR) have been defined as free-living soil bacteria dwelling in the rhizosphere and endowed with the potential to stimulate plant growth and crop yield. A plethora of reviews exhaustively documents almost all aspects of PGPR. PGPR, through their direct and indirect effects, can bring about substantial plant growth promotion (PGP). They act directly by facilitating nitrogen absorption and assimilation, mineral solubilization, production of phytohormones. Indirectly, PGPR, through their biocontrol mechanisms, produce siderophores, lytic enzymes, antibiotics, 1-aminocyclopropane-1-carboxylic acid (ACC), guarding host plants against pathogens.

35Several studies reported Acidobacteria to be avid rhizosphere colonizers. The first evidence for PGP by Acidobacteria subdivision 1 members was provided by. Their experiments confirmed interactions between three acidobacterial strains belonging to the genera Granulicella and Acidicapsa and the host plant Arabidopsis thaliana. Determination of in vitro PGP traits provided evidence that all the test strains were active producers of phytohormones IAA and siderophore. There was a significant increase in root growth parameters, although shoot biomass variations were non-significant in comparison to the controls. All three strains were able to adhere to roots, form a biofilm, and grow along the root surface. The pioneering study provided the first time with a direct confirmation regarding the Acidobacteria-plant interactions and PGP by Acidobacteria members. Acidobacteria subdivision 1 member dominates among other subdivisions, followed by subdivisions 4, 3, 8, and 23. Their preponderance in the soil environment in comparison with other subdivisions and their genetic profiles surmise their active roles in plant-soil ecosystems. Also, analysis of biosynthetic gene pathways from few publicly available genomes of soil-inhabiting acidobacterial isolates suggests the presence of genes linked to the production of secondary metabolites involved in plant growth.

36The diversity and composition analysis of broomcorn millet rhizosphere using 16S rDNA sequencing indicated Acidobacteria to be a core bacterial component among rhizobacterial assemblages, comprising 10.7% of the total operational taxonomic units (OTUs) obtained. In another interesting study, explored the effects of three PGPR strains viz., Sphingobacterium sp., Variovorax sp., and Roseomonas sp. on crop rhizospheric population densities of acidobacterial members. They reported that the equivalent cell numbers of Acidobacteria members gradually increased over time with a simultaneous increase in plant growth promotion by PGPR inocula. The study speculated the existence of beneficial interactions between the triad of difficult-to-culture bacteria, PGPR, and host plants. Additional experiments in plant-soil ecosystems are still required for unveiling the exact ecological roles of rhizospheric Acidobacteria members.

37Soil represents a luxurious pool of microorganisms, including the shadow biosphere dwellers, the difficult-to-culture bacteria which might be strategic sources for novel and successful biotechnological products. Acidobacteria is an important and among the most abundant difficult-to-culture phylum harboring the soil ecosystem. Acidobacteria plays significant ecological roles, as evidenced through their active participation in key carbon, nitrogen, and sulfur biogeochemical circuits. At the same time, the production of EPS further strengthens their ecophysiological functions in establishing plant-soil beneficial interactions. Since this divergent phylum predominates rhizosphere microbial communities, these bacteria might be a significant component of the crop’s natural environment. Initiatives for manipulating crop rhizosphere with acidobacterial populations to increase plant growth in laboratory and greenhouse studies could be considered to be future challenges and thrust areas for research. The correlation and information presented in this review might prove to be relevant for future modeling of experiments to expose the potential biotechnological roles of Acidobacteria members and exploit them as prospective alternatives to agrochemicals, facilitating sustainable agriculture.

38SK and AB contributed equally to the conception and design of the review and wrote the first draft of the manuscript. IA and RS critically reviewed and edited the manuscript. HE-E, DD, and NS wrote portions of the manuscript. All authors read and approved the final version of the manuscript.

39The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.