Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes

The prokaryotic organisms can be divided into two main groups depending upon whether their cell envelopes contain one membrane (monoderms) or two membranes (diderms). It is important to understand how these and other variations that are observed in the cell envelopes of prokaryotic organisms have originated. In 2009, James Lake proposed that cells with two membranes (primarily Gram-negative bacteria) originated from an ancient endosymbiotic event involving an Actinobacteria and a Clostridia (Lake 2009). However, this Perspective argues that this proposal is based on a number of incorrect assumptions and the data presented in support of this model are also of questionable nature. Thus, there is no reliable evidence to support the endosymbiotic origin of double membrane bacteria. In contrast, many observations suggest that antibiotic selection pressure was an important selective force in prokaryotic evolution and that it likely played a central role in the evolution of diderm (Gram-negative) bacteria. Some bacterial phyla, such as Deinococcus-Thermus, which lack lipopolysaccharide (LPS) and yet contain some characteristics of the diderm bacteria, are postulated as evolutionary intermediates (simple diderms) in the transition between the monoderm bacterial taxa and the bacterial groups that have the archetypal LPS-containing outer cell membrane found in Gram-negative bacteria. It is possible to distinguish the two stages in the evolution of diderm-LPS cells (viz. monoderm bacteria → simple diderms lacking LPS → LPS containing archetypal diderm bacteria) by means of conserved inserts in the Hsp70 and Hsp60 proteins. The insert in the Hsp60 protein also distinguishes the traditional Gram-negative diderm bacterial phyla from atypical taxa of diderm bacteria (viz. Negativicutes, Fusobacteria, Synergistetes and Elusimicrobia). The Gram-negative bacterial phyla with an LPS-diderm cell envelope, as defined by the presence of the Hsp60 insert, are indicated to form a monophyletic clade and no loss of the outer membrane from any species from this group seems to have occurred. This argues against the origin of monoderm prokaryotes from diderm bacteria by loss of outer membrane.     

One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide

How, when and why the transition between cell envelopes with one membrane (Gram-positives or monoderms) and two (Gram-negative or diderms) occurred in Bacteria is a key unanswered question in evolutionary biology. Different hypotheses have been put forward, suggesting that either the monoderm or the diderm phenotype is ancestral. The existence of diderm members in the classically monoderm Firmicutes challenges the Gram-positive/Gram-negative divide and provides a great opportunity to tackle the issue. In this review, we present current knowledge on the diversity of bacterial cell envelopes, including these atypical Firmicutes. We discuss how phylogenomic analysis supports the hypothesis that the diderm cell envelope architecture is an ancestral character in the Firmicutes, and that the monoderm phenotype in this phylum arose multiple times independently by loss of the outer membrane. Given the overwhelming distribution of diderm phenotypes with respect to monoderm ones, this scenario likely extends to the ancestor of all bacteria. Finally, we discuss the recent development of genetic tools for Veillonella parvula, a diderm Firmicute member of the human microbiome, which indicates it as an emerging new experimental model to investigate fundamental aspects of the diderm/monoderm transition.     

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an “Assembling the Tree of Life” project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium''s thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced.     

Quantitative comparison of bacterial communities in two Mediterranean sponges

Marine sponges can host in their tissues abundant and diverse bacterial communities. Lack of truly quantitative data on bacterial abundance and dynamics limits our understanding of the organization and functioning of these endobiotic communities. In this technical note, we describe a quantitative polymerase chain reaction approach to quantify the relative abundance of multiple clades of three major sponge-associated bacterial phyla: Chloroflexi, Acidobacteria, and Actinobacteria. To test our approach we used the Mediterranean sponges Spongia lamella and Aplysina aerophoba. We designed five out of the six primer sets used in our study. We tested the new primer sets for specificity and optimized their conditions. Our preliminary data showed that Spongia lamella had larger bacterial abundance than Aplysina aerophoba, except for one clade of Chloroflexi. The two Chloroflexi clades investigated in our study amplified a fraction of the Chloroflexi present in Spongia lamella and most of what is present in Aplysina aerophoba, suggesting a more diverse Chloroflexi population in Spongia lamella than in Aplysina aerophoba. This quantitative technique has a great potential to provide a rapid and robust assessment of sponge microbial target and could contribute to deciphering the complexity of these largely unknown host-symbiont interactions.     

Microbial diversity in hypersaline wastewater: the example of tanneries

In contrast to conventional wastewater treatment plants and saline environments, little is known regarding the microbial diversity of hypersaline wastewater. In this study, the microbial communities of a hypersaline tannery effluent, and those of three treatment systems operating with the tannery effluent, were investigated using 16S rDNA phylogenetic markers. The comparative analysis of 377 bacterial sequences revealed the high diversity of this type of hypersaline environment, clustering within 193 phylotypes (≥ 97% similarity) and covering 14 of the 52 divisions of the bacterial domain, i.e. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chlorobi, Planctomycetes, Spirochaetes, Synergistes, Chloroflexi, Thermotogae, Verrucomicrobia, OP3, OP11 and TM7. Most of the phylotypes were related to halophilic and pollutant-degrading bacteria. Using statistical analysis, the diversity of this type of environment was compared to that of other environmental samples selected on the basis of their salinity, oxygen content and organic load.     

Constructing and deconstructing the bacterial cell wall

The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell‐wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre‐eminent class of antibiotics—the β‐lactams, exemplified by the penicillins and cephalosporins—from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the β‐lactams is bacterial cell‐wall destruction. In the monoderm (single membrane, Gram‐positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a β‐lactam‐unreactive transpeptidase enzyme that functions in cell‐wall construction. In the diderm (dual membrane, Gram‐negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical β‐lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell‐wall construction and cell‐wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of β‐lactams. This review summarizes how the β‐lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.     

The effect of co-substrate activation on indigenous and bioaugmented PCB dechlorinating bacterial communities in sediment microcosms

Microbial reductive dechlorination by members of the phylum Chloroflexi, including the genus Dehalococcoides, may play an important role in natural detoxification of highly chlorinated environmental pollutants, such as polychlorinated biphenyls (PCBs). Previously, we showed the increase of an indigenous bacterial population belonging to the Pinellas subgroup of Dehalococcoides spp. in Anacostia River sediment (Washington DC, USA) microcosms treated with halogenated co-substrates (“haloprimers”), tetrachlorobenzene (TeCB), or pentachloronitrobenzene (PCNB). The PCNB-amended microcosms exhibited enhanced dechlorination of weathered PCBs, while TeCB-amended microcosms did not. We therefore developed and used different phylogenetic approaches to discriminate the effect of the two different haloprimers. We also developed complementary approaches to monitor the effects of haloprimer treatments on 12 putative reductive dehalogenase (rdh) genes common to Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain CBDB1. Our results indicate that 16S rRNA gene-based phylogenetic analyses have a limit in their ability to distinguish the effects of two haloprimer treatments and that two of rdh genes were present in high abundance when microcosms were amended with PCNB, but not TeCB. rdh gene-based phylogenetic analysis supports that these two rdh genes originated from the Pinellas subgroup of Dehalococcoides spp., which corresponds to the 16S rRNA gene-based phylogenetic analysis.     

Borrelia burgdorferi locus BB0795 encodes a BamA orthologue required for growth and efficient localization of outer membrane proteins

The outer membrane (OM) of the pathogenic diderm spirochete, Borrelia burgdorferi, contains integral β‐barrel outer membrane proteins (OMPs) in addition to its numerous outer surface lipoproteins. Very few OMPs have been identified in B. burgdorferi, and the protein machinery required for OMP assembly and OM localization is currently unknown. Essential OM BamA proteins have recently been characterized in Gram‐negative bacteria that are central components of an OM β‐barrel assembly machine and are required for proper localization and insertion of bacterial OMPs. In the present study, we characterized a putative B. burgdorferi BamA orthologue encoded by open reading frame bb0795. Structural model predictions and cellular localization data indicate that the B. burgdorferi BB0795 protein contains an N‐terminal periplasmic domain and a C‐terminal, surface‐exposed β‐barrel domain. Additionally, assays with an IPTG‐regulatable bb0795 mutant revealed that BB0795 is required for B. burgdorferi growth. Furthermore, depletion of BB0795 results in decreased amounts of detectable OMPs in the B. burgdorferi OM. Interestingly, a decrease in the levels of surface‐exposed lipoproteins was also observed in the mutant OMs. Collectively, our structural, cellular localization and functional data are consistent with the characteristics of other BamA proteins, indicating that BB0795 is a B. burgdorferi BamA orthologue.     

Salinity controls soil microbial community structure and function in coastal estuarine wetlands

Soil salinity acts as a critical environmental filter on microbial communities, but the consequences for microbial diversity and biogeochemical processes are poorly understood. Here, we characterized soil bacterial communities and microbial functional genes in a coastal estuarine wetland ecosystem across a gradient (~5 km) ranging from oligohaline to hypersaline habitats by applying the PCR-amplified 16S rRNA (rRNA) genes sequencing and microarray-based GeoChip 5.0 respectively. Results showed that saline soils in marine intertidal and supratidal zone exhibited higher bacterial richness and Faith's phylogenetic diversity than that in the freshwater-affected habitats. The relative abundance of taxa assigned to Gammaproteobacteria, Bacteroidetes and Firmicutes was higher with increasing salinity, while those affiliated with Acidobacteria, Chloroflexi and Cyanobacteria were more prevalent in wetland soils with low salinity. The phylogenetic inferences demonstrated the deterministic role of salinity filtering on the bacterial community assembly processes. The abundance of most functional genes involved in carbon degradation and nitrogen cycling correlated negatively with salinity, except for the hzo gene, suggesting a critical role of the anammox process in tidal affected zones. Overall, the salinity filtering effect shapes the soil bacterial community composition, and soil salinity act as a critical inhibitor in the soil biogeochemical processes in estuary ecosystems.     

黑龙江省表层冻土细菌群落结构组成和功能特征

冻土是气候变化的敏感区,冻土中细菌对于预测冻土和气候之间的潜在反馈机制至关重要,研究冻土区土壤中细菌的多样性和种群结构将有助于及时检测环境变化并采取有效的应对措施。以黑龙江省表层冻土为研究对象,运用Illumina MiSeq高通量测序分析技术,系统分析黑龙江表层冻土细菌群落结构组成和功能特征,探究影响因素。结果表明,得到的785640条原始序列可划分为30个门,109个纲,209个目,326个科,512个属,598个种。优势菌门主要包括Proteobacteria、Actinobacteria、Acidobacteria、Chloroflexi、Bacteroidetes、Verrucomicrobia,在P<0.01水平上,Proteobacteria与Actinobacteria、Chloroflexi极显著负相关,与Acidobacteria极显著正相关,Actinobacteria与Acidobacteria极显著负相关,与Chloroflexi极显著正相关,Acidobacteria和Chloroflexi之间则无显著相关性。属水平上,Aetherobacter属在各...     

Rapid qualitative characterization of bacterial community in eutrophicated wastewater stabilization plant by T-RFLP method based on 16S rRNA genes

Waste stabilization ponds are a simple, low-cost extensive process for treating wastewater, and well adapted to low socio-economic conditions in developing countries where the microbial populations in these systems are not well characterized. The phylogenetic bacterial community structure within a Tunisian wastewater stabilization plant treating domestic wastewater was assessed by Terminal Restriction Fragment Length Polymorphism method targeting 16S rRNA genes and by the APLAUS+ software of the Microbial Community Analysis (MiCA) web based tool. The dimeric enzymatic digestion with HaeIII and HinfI restriction enzymes revealed high bacterial diversity within the plant where 11 bacterial phyla were identified. The total bacterial community structure includes bacteria catalysing nitrogen and phosphorus removal and bacteria involved in the sulfur cycle. The bacterial community was characterized by the dominance of Proteobacteria which was the most populous phylum (60%) followed by the Actinobacteria (20%), the Firmicutes (10.3%), the Bacteroidetes (2.3%), the Nitrospira (2.2%). Minor bacterial phyla groups occupied smaller fractions such as Chloroflexi, Deferribacteres and Verrumicrobia. T-RFLP analysis revealed also that The Proteobacteria phylum was characterized by the dominance of bacteria of The Gammaproteobacteria class.     

Microbial Communities in Chesapeake & Ohio Canal National Historical Park and Their Function as Indicators of Water Quality

Abstract

The objective of this study was to establish meaningful relationships between prokaryotic community profiles and water quality parameters in different water bodies (spring, stream, cave, and mine) in the middle reach of the Chesapeake & Ohio Canal National Historic Park (C&O), Maryland. The microbial profiles in the water samples were determined using metagenomic analysis. The relationships between microbial phylogenetic profiles and water quality parameters were investigated using principal component analysis (PCA) and redundancy analysis (RDA). The most abundant phyla identified in most samples were Proteobacteria (55.4%), Bacteroidetes (12.3%), Actinobacteria (10.6%), Firmicutes (2.4%), Planktomycetes (1.8%), Verrucomicrobia (1.5%), Chloroflexi (1.5%), and Acidobacteria (1.3%), which are major bacterial and archaeal groups typically observed in natural freshwater environments. PCA showed that water chemistry was determined primarily by the geology of the site and the type of water source (i.e., spring, stream, cave, or mine). Most samples located in carbonate formations correlated with high alkalinity, inorganic carbon, and calcium, representing the typical karstic geochemistry. RDA shows that pH, electrical conductivity, temperature and nutrients including nitrate, phosphate, and sulfate, were significant determinants of the microbial ecology.     

Use of mulberry–soybean intercropping in salt–alkali soil impacts the diversity of the soil bacterial community

Diverse intercropping system has been used to control disease and improve productivity in the field. In this research, the bacterial communities in salt–alkali soils of monoculture and intercropping mulberry and soybean were studied using 454‐pyrosequencing of the 16S rDNA gene. The dominant taxonomic groups were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Planctomycetes and Gemmatimonadetes and these were present across all samples. However, the diversity and composition of bacterial communities varied between monoculture and intercropping samples. The estimated bacterial diversity (H') was higher with intercropping soybean than in monoculture soybean, whereas H' showed an opposite pattern in monoculture and intercropping mulberry. Populations of Actinobacteria, Acidobacteria, and Proteobacteria were variable, depending on growth of plants as monoculture or intercropped. Most of Actinobacteria and Chloroflexi were found in intercropping samples, while Acidobacteria and Proteobacteria were present at a higher percentage in monoculture samples. The plant diversity of aboveground and microbial diversity of belowground was linked and soil pH seemed to influence the bacterial community. Finally, the specific plant species was the major factor that determined the bacterial community in the salt–alkali soils.     

Phylogenetic Diversity and Axial Distribution of Microbes in the Intestinal Tract of the Polychaete <Emphasis Type="Italic">Neanthes glandicincta</Emphasis>

The phylogenetic diversity and axial distribution of microorganisms in three sections of the gastrointestinal tracts of the polychaete Neanthes glandicincta was evaluated using both most probable number method and cloning analyses of 16S rRNA genes in this study. Quantification of the density of microorganisms in the gut showed that aerobic microorganisms decreased from anterior to posterior, while anaerobic ones showed a reverse trend. The total numbers of microorganisms decreased significantly (p < 0.05, analysis of variance) but more rapidly from the anterior to the middle segment. Phylogenetic analysis showed that the dominating phylogenetic groups included Methanomicrobiales I: Methanosaetaceae (up to 66% of archaeal clones), δ-Proteobacteria (up to 42% of bacterial clones), and γ-Proteobacteria (up to 30% of bacterial clones) widely distributed throughout the entire gut. Other microbiota distributed in different gut sections were Methanomicrobiales II: Methanospirillaceae, Methanomicrobiales III, Thermoplasmatales, Crenarchaea, Methanobacteriaceae, and Methanosarcinales for archaea; and α-Proteobacteria, β-Proteobacteria, Fusobacteria, Clostridia, Chloroflexi, and Planctomycetes for bacteria. The results reveal a difference in microbial community structure along the gut of N. glandicincta. The various phylogenetic diversity and axial distribution of microbes along the gut might indicate an environmental gradient from anterior to posterior sections affecting the structure of the microbial community.     

What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms

The evolutionary relationship within prokaryotes is examined based on signature sequences (defined as conserved inserts or deletions shared by specific taxa) and phylogenies derived from different proteins. Archaebacteria are indicated as being monophyletic by a number of proteins related to the information transfer processes. In contrast, for several other highly conserved proteins, common signature sequences are present in archaebacteria and Gram-positive bacteria, whereas Gram-negative bacteria are indicated as being distinct. For these proteins, archaebacteria do not form a phylogenetically distinct clade but show polyphyletic branching within Gram-positive bacteria. A closer relationship of archaebacteria to Gram-positive bacteria in comparison with Gram-negative bacteria is generally seen for the majority of the available gene/protein sequences. To account for these results and the fact that both archaebacteria and Gram-positive bacteria are prokaryotes surrounded by a single cell membrane, I propose that the primary division within prokaryotes is between monoderm prokaryotes (surrounded by a single membrane) and diderm prokaryotes (i.e. all true Gram-negative bacteria containing both an inner cytoplasmic membrane and an outer membrane). This proposal is consistent with both cell morphology and signature sequences in different proteins. The monophyletic nature of archaebacteria for some genes, and their polyphyletic branching within Gram-positive bacteria as suggested by others, is critically examined, and several explanations, including derivation of archaebacteria from Gram-positive bacteria in response to antibiotic selection pressure, are proposed. Signature sequences in proteins also indicate that the low-G + C Gram-positive bacteria are phylogenetically distinct from the high-G + C Gram-positive group and that the diderm prokaryotes (i.e. Gram-negative bacteria) appear to have evolved from the latter group. Protein phylogenies and signature sequences also show that all eukaryotic cells have received significant gene contributions from both an archaebacterium and a Gram-negative eubacterium. Thus, the hypothesis that archaebacteria and eukaryotes shared a common ancestor exclusive of eubacteria is not supported. These observations provide evidence for an alternate view of the evolutionary relationship among living organisms that is different from the currently popular three-domain proposal.     

ERC-group microflex: microbiology of Dehalococcoides-like Chloroflexi

The Microflex project, funded within the first call of the European Research Council, focuses on a specific group of bacteria, the Dehalococcoides-like Chloroflexi. This group of bacteria deeply rooting in the phylogenetic tree is formed by several cultivated strains of the proposed genus “Dehalococcoides” and many sequences of uncultivated organisms mostly from marine sediments or terrestrial subsurface locations. The project compares cultivated Dehalococcoides species growing by organohalide respiration using halogenated compounds as electron acceptors with marine Chloroflexi populations. For this comparison a wide array of different approaches and techniques are used including cultivation, biochemical analyses, molecular tools and isotopic fractionation measurements. The project aims at contributing to the understanding of the physiology of Dehalococcoides-like Chloroflexi in deep marine sediments and their mode of living. A second aim of the project is the further understanding of the physiology and biochemistry of dehalogenating Dehalococcoides species and how these bacteria can be used efficiently for bioremediation of contaminated subsurface environments.     

Bacterial communication through membrane vesicles

ABSTRACT

Bacteria can communicate through diffusible signaling molecules that are perceived by cognate receptors. It is now well established that bacterial communication regulates hundreds of genes. Hydrophobic molecules which do not diffuse in aqueous environments alone have been identified in bacterial communication, that raised the question on how these molecules are transported between cells and trigger gene expressions. Recent studies show that these hydrophobic signaling molecules, including a long-chain N-acyl homoserine lactone signal produced in Paracoccus denitrificans, are carried by membrane vesicles (MVs). MVs were thought to be formed only through the blebbing of the cell membrane, but new findings in Pseudomonas aeruginosa and Bacillus subtilis revealed that different types of MVs can be formed through explosive cell lysis or bubbling cell death, which findings have certain implications on our view of bacterial interactions.     

Towards a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing ‘phyloh’ as a novel phylogenetic diversity analysis tool

The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh ) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh , was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity.     

Molecular Characterization of Prokaryotic Communities Associated with Lonar Crater Basalts

The Lonar crater is an unusually well-preserved meteorite impact structure that is located in one of the largest volcanic provinces on Earth (i.e., the Deccan Traps in India). The diversity of endoliths in Lonar crater basalts or Deccan flood basalts is not known. Here, the phylogenetic diversity of endolithic Bacteria and Archaea inhabiting basalts retrieved from four discrete sampling sites on the Lonar crater walls and the lake-bed was assessed using culture-independent molecular methods. Taxonomic classification of 16S rRNA gene sequences from all four basalt samples revealed similarities as well as dissimilarities in the presence or absence of several prokaryotic taxa. Cluster analysis of Denaturing gradient gel electrophoresis fingerprints and UniFrac analysis of clone library sequences suggested substantial variations in bacterial and archaeal diversity between crater-wall and lake-bed sites. Although sequences affiliated to the bacterial phyla Actinobacteria, Acidobacteria and Chloroflexi were relatively more abundant in crater-wall basalts than in lake-bed basalts; the reverse was observed for sequences related to Proteobacteria, Firmicutes, Cyanobacteria and Bacteroidetes. Archaea in crater-wall and lake-bed basalt libraries were almost completely represented by Thaumarchaeota and Euryarchaeota, respectively. Diversity indices and richness estimates suggested the diversity of endolithic Bacteria to be higher than that of Archaea in the Lonar crater basalts. A substantial number of clone library sequences did not affiliate with extant Bacteria and Archaea. The detection of several putative lineages associated with C, N and S cycling suggests that the Lonar crater basalts are colonized by metabolically diverse prokaryotic communities involved in biogeochemical cycling of major elements.