Olive-Mill Wastewater Bacterial Communities Display a Cultivar Specific Profile

Culture-dependent and -independent approaches were employed to identify the bacterial community structure from olive-mill wastewater produced from three olive-fruit varieties. The 233 bacterial isolates recovered were phylogenetically related to 38 members of Firmicutes, Actinobacteria, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, and Bacteroidetes. Employing a novel microarray-based approach (PhyloChip) a high bacterial diversity was revealed consisting of 18 different phyla with representatives from 99 different families. The bacterial diversity in olive-mill wastewater from the three olive tree varieties was dominated by α-, β-, γ-, δ-, ε-Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Cyanobacteria, and Actinobacteria. This in-depth analysis of the indigenous microbiota indicated a cultivar-specific bacterial profile. Interestingly, the common bacterial taxa present in all three varieties examined were restricted indicating that the bacterial communities present in the olive-mill wastewater are greatly influenced by the olive-fruit variety.     

Analysis of Bacterial Community Composition of a Spring Water from the Western Ghats,India Using Culture Dependent and Molecular Approaches

Cultivation based and culture independent molecular approaches were used to characterize the composition and structure of bacterial community from a natural warm spring in the Western Ghats, a biodiversity ‘hotspot’. Dilution plating was done on three types of media with varying nutrient levels. Relatively nutritionally poor medium supported growth of highest number of bacteria (4.98 × 10³ ml⁻¹) compared to nutritionally rich media. On the basis of different morphological features on the plate, 62 aerobic and heterotrophic bacterial strains were isolated and their 16S rRNA genes were sequenced and analyzed. On the basis of sequence similarity these isolates were found to be distributed in 21 different genera belonging to Proteobacteria (58%) followed by Firmicutes (26%), Actinobacteria (13%) and Bacteroidetes (3%). Amplification of 16S rRNA gene of the community DNA using eubacterial primers, followed by cloning and sequencing revealed that predominant members of the habitat belong to the phylum Cyanobacteria (60%) followed by Proteobacteria (19.5%), Bacteroidetes (6.67%), Actinobacteria (4.4%) and Firmicutes (2.2%) and small ribosomal subunit of a plastid (of Chlorophyta, 2.2%).     

Cultivable Bacterial Community from South China Sea Sponge as Revealed by DGGE Fingerprinting and 16S rDNA Phylogenetic Analysis

The cultivable bacterial communities associated with four South China Sea sponges—Stelletta tenuis, Halichondria rugosa, Dysidea avara, and Craniella australiensis in mixed cultures—were investigated by microbial community DNA-based DGGE fingerprinting and 16S rDNA phylogenetic analysis. Diverse bacteria such as α-, γ-, δ-Proteobacteria, Bacteroidetes, and Firmicutes were cultured, some of which were previously uncultivable bacteria, potential novel strains with less than 95% similarity to their closest relatives and sponge symbionts growing only in the medium with the addition of sponge extract. According to 16S rDNA BLAST analysis, most of the bacteria were cultured from sponge for the first time, although similar phyla of bacteria have been previously recognized. The selective pressure of sponge extract on the cultured bacterial species was suggested, although the effect of sponge extract on bacterial community in high nutrient medium is not significant. Although α- and γ-Proteobacteria appeared to form the majority of the dominant cultivable bacterial communities of the four sponges, the composition of the cultivable bacterial community in the mixed culture was different, depending on the medium and sponge species. Greater bacterial diversity was observed in media C and CS for Stelletta tenuis, in media F and FS for Halichondria rugosa and Craniella australiensis. S. tenuis was found to have the highest cultivable bacterial diversity including α-, γ-, δ-Proteobacteria, Bacteroidetes, and Firmicutes, followed by sponge Dysidea avara without δ-Proteobacteria, sponge Halichondria rugosa with only α-, γ-Proteobacteria and Bacteroidetes, and sponge C. australiensis with only α-, γ-Proteobacteria and Firmicutes. Based on this study, by the strategy of mixed cultivation integrated with microbial community DNA-based DGGE fingerprinting and phylogenetic analysis, the cultivable bacterial community of sponge could be revealed effectively.     

Impact of the Maize Rhizosphere on the Genetic Structure, the Diversity and the Atrazine-degrading Gene Composition of Cultivable Atrazine-degrading Communities

Sixty-six atrazine-degrading bacterial communities utilizing atrazine as sole N source and citrate as principal C source were isolated from unplanted and maize planted soils treated with atrazine. Ribosomal intergenic spacer analysis (RISA) fingerprints revealed that the genetic structure of atrazine-degrading bacterial communities was modified in the maize rhizosphere. To assess the underlying microbial diversity, 16S rDNA sequences amplified from each bacterial community were cloned. Libraries containing 660 16S rDNA clones were screened by restriction fragment length polymorphism (RFLP) analysis. In all, 63 clone families were identified. Rarefaction curves did not reach a clear saturation, indicating that the analysis of a greater number of clones would have revealed further diversity. Recovered 16S rDNA sequences were related to Actinobacteria, Bacteroidetes and Proteobacteria. The four dominant RFLP families were highly similar to Variovorax paradoxus, Burkholderia cepacia, Arthrobacter sp. and Bosea sp. The composition of most of the atrazine-degrading bacterial communities consisted of 2–7 different bacterial species. Various atrazine-degrading gene compositions were observed, two of these atzABCDEF, trzND and atzBCDEF, trzN being largely dominant. The first was more frequently detected in bacterial communities isolated from the maize rhizosphere whereas the second was more frequently detected in communities isolated from bulk soil. Monitoring of atrazine-degrading activity showed that 76% of the bacterial communities degraded up to 80% of the initially added atrazine within 15 days of culture. Altogether our results indicate that the maize rhizosphere has an impact on the genetic structure, the diversity and atrazine-degrading gene composition of the atrazine-degrading communities.     

Molecular Analyses of the Microbial Community Composition of an Anoxic Basin of a Municipal Wastewater Treatment Plant Reveal a Novel Lineage of Proteobacteria

A culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anoxic activated sludge from a municipal wastewater treatment plant. Two 16S rRNA gene libraries were constructed using total genomic DNA and amplified by polymerase chain reaction using primers specific for archaeal or bacterial domains. Phylogenetic analysis of 132 and 249 almost full-length 16S rRNA genes for Archaea and Bacteria, respectively, was done using the ARB software package. Phylogenetic groups affiliated with the Archaea belong to Euryarchaeota (93.8% of the operational taxonomic units [OTUs]) and Crenarchaeota (6.2% of the OTUs). Within the bacterial library, 84.8% of the OTUs represent novel putative phylotypes never described before and affiliated with ten divisions. The Proteobacteria phylum is the most abundant and diversified phylogenetic group representing 60.4% of the OTUs, followed by Bacteroidetes (22.1%) and gram-positives (6.1%). Interestingly, we detected a novel Proteobacteria monophyletic group distinct from the five known subclasses, which we named New Lineage of Proteobacteria (NLP) lineage, and it is composed of eight clones representing 4.6% of the Proteobacteria. A new 16S rRNA-targeted hybridization probe was designed and fluorescent in situ hybridization analyses shows representatives of NLP as cocci-shaped microorganisms. The Chloroflexi, Acidobacterium, and Nitrospira phyla and TM7 candidate division are each represented by ≤3% of clone sequences. A comprehensive set of eight 16S and 23S rRNA-targeted oligonucleotide probes was used to quantify these major groups by dot blot hybridization within 12 samples. The Proteobacteria accounted for 82.5 ± 4.9%, representing the most abundant phyla. The Bacteroidetes and Planctomycetales groups accounted for 4.9 ± 1.3% and 4 ± 1.7%, respectively. Firmicutes and Actinobacteria together accounted for only 1.9 ± 0.5%. The set of probes covers 93.4 ± 14% of the total bacterial population rRNA within the anoxic basin.     

Archaeal and bacterial communities of heavy metal contaminated acidic waters from zinc mine residues in Sepetiba Bay

Mining of metallic sulfide ore produces acidic water with high metal concentrations that have harmful consequences for aquatic life. To understand the composition and structure of microbial communities in acid mine drainage (AMD) waters associated with Zn mine tailings, molecular diversity of 16S genes was examined using a PCR, cloning, and sequencing approach. A total of 78 operational taxonomic units (OTUs) were obtained from samples collected at five different sites in and around mining residues in Sepetiba Bay, Brazil. We analyzed metal concentration, physical, chemical, and microbiological parameters related to prokaryotic diversity in low metal impacted compared to highly polluted environments with Zn at level of gram per liter and Cd–Pb at level of microgram per liter. Application of molecular methods for community structure analyses showed that Archaea and Bacteria groups present a phylogenetic relationship with uncultured environmental organisms. Phylogenetic analysis revealed that bacteria present at the five sites fell into seven known divisions, α-Proteobacteria (13.4%), β-Proteobacteria (16.3%), γ-Proteobacteria (4.3%), Sphingobacteriales (4.3%), Actinobacteria (3.2%) Acidobacteria (2.1%), Cyanobacteria (11.9%), and unclassified bacteria (44.5%). Almost all archaeal clones were related to uncultivated Crenarchaeota species, which were shared between high impacted and low impacted waters. Rarefaction curves showed that bacterial groups are more diverse than archaeal groups while the overall prokaryotic biodiversity is lower in high metal impacted environments than in less polluted habitats. Knowledge of this microbial community structure will help in understanding prokaryotic diversity, biogeography, and the role of microorganisms in zinc smelting AMD generation and perhaps it may be exploited for environmental remediation procedures in this area.     

Incorporation of 3H-Thymidine by Different Prokaryotic Groups in Relation to Temperature and Nutrients in a Lacustrine Ecosystem

The incorporation of [³H-methyl] thymidine (³H-TdR) by Eubacteria, bacterial groups (α- and β-Proteobacteria, Cytophaga–Flavobacter), and Archaea was measured according to temperature (7 and 17°C) and nutrient levels (nitrogen, phosphorus, and carbon) in a lacustrine system (Sep, France). Short-term incubation was performed using a combination of microautoradiography and fluorescent in situ hybridization. Irrespective of the temperatures and nutrients studied, all the major phylogenetic bacterial groups assimilated ³H-TdR, and in most of the treatments studied, the proportion of β-Proteobacteria taking up ³H-TdR was higher than those in the other bacterial groups. The proportion of Bacteria and different bacterial groups studied incorporating ³H-TdR were significantly increased, approximately 1.5-fold, by temperature except for α-Proteobacteria (7.6-fold). The nutrient effect was not the same for the different bacterial groups according to the temperatures studied. The proportions of α-Proteobacteria (at both temperatures) and Cytophaga–Flavobacter (at 7°C) taking up ³H-TdR were significantly decreased and increased by adding N and P, respectively. Also, adding N, P, and C increased and decreased the percentage of β-Proteobacteria incorporating ³H-TdR at 7 and 17°C, respectively. The archaeal community showed a similar proportion of active cells (i.e., ³H-TdR) to the bacterial community, and uptake of ³H-TdR by Archaea was significantly increased (P < 0.05) by both temperature and nutrients. Thus, the assimilation of ³H-TdR by bacterial groups and Archaea in lacustrine system is significantly controlled by both temperature and nutrients.     

Proteobacteria and Bacteroidetes are major phyla of filterable bacteria passing through 0.22 μm pore size membrane filter,in Lake Sanaru,Hamamatsu, Japan

141 filterable bacteria that passed through a 0.22 μm pore size filter were isolated from Lake Sanaru in Hamamatsu, Japan. These belonged to Proteobacteria, Bacteroidetes, Firmicutes, or Actinobacteria among which the first two phyla comprised the majority of the isolates. 48 isolates (12 taxa) are candidates assignable to new bacterial species or genera of Proteobacteria or Bacteroidetes.     

Diversity of 16S rRNA genes in metagenomic community of the freshwater sponge Lubomirskia baicalensis

Phylogenetic analysis of the nucleotide sequences of 16S rRNA genes in the metagenomic community of Lubomirskia baicalensis has revealed taxonomic diversity of bacteria associated with the endemic freshwater sponge. Fifty-four operational taxonomic units (OTUs) belonging to six bacterial phyla (Actinobacteria, Proteobacteria (class ??-Proteobacteria and ??-Proteobacteria) Verrucomicrobia, Bacteroidetes, Cyanobacteria, and Nitrospira) have been identified. Actinobacteria, whose representatives are known as antibiotic producers, is the dominant phylum of the community (37%, 20 OTUs). All sequences detected shared the maximal homology with unculturable microorganisms from freshwater habitats. The wide diversity of bacteria closely coexisting with the Baikal sponge indicate the complex ecological relationships in the community formed under the unique conditions of Lake Baikal.     

Microbial diversity in acid mineral bioleaching systems of dongxiang copper mine and Yinshan lead–zinc mine

To understand the composition and structure of microbial communities in acid mineral bioleaching systems, the molecular diversity of 16S rDNA genes was examined using a PCR-based cloning approach. A total of 31 Operational Taxonomic Units (OTUs) were obtained from the four samples taken from four different bioleaching sites in Yinshan lead–zinc mine and Dongxiang copper mine in Jiangxi Province, China. The percentages of overlapping OTUs between sites ranged from 22.2 to 50.0%. Phylogenetic analysis revealed that the bacteria present at the four bioleaching sites fell into six divisions, α-Proteobacteria (1.1%), β-Proteobacteria (2.3%), γ-Proteobacteria (30.8%), Firmicutes (15.4%), Actinobacteria (0.3%) and Nitrospira (50.1%). Organisms of genera Leptospirillum, Acidithiobacillus, and Sulfobacillus, which were in Nitrospira, γ-Proteobacteria, and Firmicutes divisions, respectively, were the most dominant. The results of principal component analysis based on the six phylogenetic divisions and biogeochemical data indicated that the microbial community structure of a site was directly related to the biogeochemical characteristic of that site. It follows therefore that sites with similar biogeochemical characteristics were comprised of similar microbial community structures. The results in our study also suggest that the elements copper and arsenic appear to be the key factors affecting the compositions and structures of microbial community in the four bioleaching sites. Zhiguo He, Shengmu Xiao, Xuehui Xie are equally contributed to this work.     

Bacterial community structure within an activated sludge reactor added with phenolic compounds

Biodegradation of phenolic compounds in bioreactors is well documented, but the changes in the bacterial populations dynamics during degradation were not that often. A glass bubble column used as reactor was inoculated with activated sludge, spiked with 2-chlorophenol, phenol and m-cresol after 28 days and maintained for an additional 56 days, while the 16S rRNA gene from metagenomic DNA was monitored. Proteobacteria (68.1%) dominated the inoculum, but the bacterial composition changed rapidly. The relative abundance of Bacteroidetes and Firmicutes decreased from 4.8 and 9.4 to <0.1 and 0.2% respectively, while that of Actinobacteria and TM7 increased from 4.8 and 2.0 to 19.2 and 16.1% respectively. Phenol application increased the relative abundance of Proteobacteria to 94.2% (mostly Brevundimonas 17.6%), while that of Bacteroidetes remained low (1.2%) until day 42. It then increased to 47.3% (mostly Leadbetterella 46.9%) at day 84. It was found that addition of phenolic compounds did not affect the relative abundance of the Alphaproteobacteria initially, but it decreased slowly while that of the Bacteroidetes increased towards the end.

     

Diversity of Gut Bacteria of <Emphasis Type="Italic">Reticulitermes flavipes</Emphasis> as Examined by 16S rRNA Gene Sequencing and Amplified rDNA Restriction Analysis

The phylogenetic species richness of the bacteria in the gut of the termite Reticulitermes flavipes was examined using near full-length 16S rRNA gene sequencing and amplified rDNA restriction analysis (ARDRA). We amplified the genes by polymerase chain reaction (PCR) directly from a mixed population of termite gut bacteria and isolated them using cloning techniques. Sequence analysis of 42 clones identified a broad taxonomic range of ribotypes from six phyla within the domain Bacteria: Proteobacteria, Spirochaetes, Bacteroidetes, Firmicutes, Actinobacteria, and the recently proposed “Endomicrobia.” Analysis of the sequence data suggested the presence of a termite specific bacterial lineage within Bacteroidetes. The ARDRA data included 261 different ARDRA profiles of 512 clones analyzed. These data suggest the gut flora in R. flavipes is extremely diverse.     

Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding

Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m⁻¹ and pH 7.80 (LOW soil), with EC 56 dS m⁻¹ and pH 10.11 (MEDIUM soil) and with EC 159 dS m⁻¹ and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the α- and γ-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.     

Unique Microbial Signatures of the Alien Hawaiian Marine Sponge Suberites zeteki

Invasive species poses a threat to the world’s oceans. Alien sponges account for the majority of introduced marine species in the isolated Hawaiian reef ecosystems. In this study, cultivation-dependent and cultivation-independent techniques were applied to investigate microbial consortia associated with the alien Hawaiian marine sponge Suberites zeteki. Its microbial communities were diverse with representatives of Actinobacteria, Firmicutes, α- and γ-Proteobacteria, Bacteroidetes, Chlamydiae, Planctomycetes, and Cyanobacteria. Specifically, the genus Chlamydia was identified for the first time from marine sponges, and two genera (Streptomyces and Rhodococcus) were added to the short list of culturable actinobacteria from sponges. Culturable microbial communities were dominated by Bacillus species (63%) and contained actinobacterial species closely affiliated with those from habitats other than marine sponges. Cyanobacterial clones were clustered with free-living cyanobacteria from water column and other environmental samples; they show no affiliation with other sponge-derived cyanobacteria. The low sequence similarity of Planctomycetes, Chlamydiae, and α-Proteobacteria clones to other previously described sequences suggested that S. zeteki may contain new lineages of these bacterial groups. The microbial diversity of S. zeteki was different from that of other studied marine sponges. This is the first report on microbial communities of alien marine invertebrate species. For the first time, it provides an insight into microbial structure within alien marine sponges in the Hawaiian marine ecosystems.     

Isolation of the exoelectrogenic denitrifying bacterium Comamonas denitrificans based on dilution to extinction

The anode biofilm in a microbial fuel cell (MFC) is composed of diverse populations of bacteria, many of whose capacities for electricity generation are unknown. To identify functional populations in these exoelectrogenic communities, a culture-dependent approach based on dilution to extinction was combined with culture-independent community analysis. We analyzed the diversity and dynamics of microbial communities in single-chamber air-cathode MFCs with different anode surfaces using denaturing gradient gel electrophoresis based on the 16S rRNA gene. Phylogenetic analyses showed that the bacteria enriched in all reactors belonged primarily to five phylogenetic groups: Firmicutes, Actinobacteria, α-Proteobacteria, β-Proteobacteria, and γ-Proteobacteria. Dilution-to-extinction experiments further demonstrated that Comamonas denitrificans and Clostridium aminobutyricum were dominant members of the community. A pure culture isolated from an anode biofilm after dilution to extinction was identified as C. denitrificans DX-4 based on 16S rRNA sequence and physiological and biochemical characterizations. Strain DX-4 was unable to respire using hydrous Fe(III) oxide but produced 35 mW/m² using acetate as the electron donor in an MFC. Power generation by the facultative C. denitrificans depends on oxygen and MFC configuration, suggesting that a switch of metabolic pathway occurs for extracellular electron transfer by this denitrifying bacterium.     

Bacterial Community Structure of Sediments of the Bizerte Lagoon (Tunisia), a Southern Mediterranean Coastal Anthropized Lagoon

In order to estimate how pollution affects the bacterial community structure and composition of sediments, chemical and molecular approaches were combined to investigate eight stations around the Bizerte lagoon. Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA genes revealed that each station was characterized by a specific bacterial community structure. The combination of this data with those of chemical analysis showed a correlation between the bacterial fingerprint and the pollutant content, principally with hydrocarbon pollution. The composition of the bacterial community of two contrasted stations related to the pollution revealed sequences affiliated to α, β, γ, δ, ε subclass of the Proteobacteria, Actinobacteria, and Acidobacteria in both stations although in different extent. Gamma and delta subclass of the Proteobacteria were dominant and represent 70% of clones in the heavy-metal-contaminated station and 47% in the polyaromatic hydrocarbon (PAH)-contaminated. Nevertheless, most of the sequences found were unaffiliated to cultured bacteria. The adaptation of the bacterial community mainly to PAH compounds demonstrated here and the fact that these bacterial communities are mainly unknown suggest that the Bizerte lagoon is an interesting environment to understand the capacity of bacteria to cope with some pollutants.     

Taxonomic and functional diversity of atrazine‐degrading bacterial communities enriched from agrochemical factory soil

Aims: To characterize atrazine‐degrading potential of bacterial communities enriched from agrochemical factory soil by analysing diversity and organization of catabolic genes. Methods and Results: The bacterial communities enriched from three different sites of varying atrazine contamination mineralized 65–80% of ¹⁴C ring‐labelled atrazine. The presence of trzN‐atzBC‐trzD, trzN‐atzABC‐trzD and trzN‐atzABCDEF‐trzD gene combinations was determined by PCR. In all enriched communities, trzN‐atzBC genes were located on a 165‐kb plasmid, while atzBC or atzC genes were located on separated plasmids. Quantitative PCR revealed that catabolic genes were present in up to 4% of the community. Restriction analysis of 16S rDNA clone libraries of the three enrichments revealed marked differences in microbial community structure and diversity. Sequencing of selected clones identified members belonging to Proteobacteria (α‐, β‐ and γ‐subclasses), the Actinobacteria, Bacteroidetes and TM7 division. Several 16S rRNA gene sequences were closely related to atrazine‐degrading community members previously isolated from the same contaminated site. Conclusions: The enriched communities represent a complex and diverse bacterial associations displaying heterogeneity of catabolic genes and their functional redundancies at the first steps of the upper and lower atrazine‐catabolic pathway. The presence of catabolic genes in small proportion suggests that only a subset of the community has the capacity to catabolize atrazine. Significance and Impact of the Study: This study provides insights into the genetic specificity and the repertoire of catabolic genes within bacterial communities originating from soils exposed to long‐term contamination by s‐triazine compounds.     

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.     

Geochemistry Shapes Bacterial Communities and their Metabolic Potentials in Tertiary Coalbed

Culture-dependent and independent approaches were used to understand the microbiota thriving in tertiary coalbed, located in Jammu and Kashmir, India. We observed changes in physicochemical properties of the surface sediment (CM1) and coalbed (CM2) which detailed the influence of environmental factors on the structure and capabilities of bacterial communities. A total of 316 bacterial isolates representing 35 genera were isolated. We noted comparable difference in uncultivable bacterial communities which revealed the predominance of Proteobacteria in both the study sites. Moreover, we observed differential abundance of phyla Actinobacteria (49.6%), Firmicutes (4.2%), and Bacteroidetes (0.8%) in CM1, whereas Actinobacteria (11%), Firmicutes (37.8%), and Bacteroidetes (2.3%) in CM2. Additionally, functional imputations using PICRUSt depicted ～30% higher assemblage of major gene families in CM1 in comparison to CM2. Bacterial communities residing at CM1 were predominantly involved in methane oxidation, whereas CM2 communities found to play a vital process of conversion of coal to biogenic-methane enabling microbes to survive under constraints of high sulfur content, salt precipitation, and low nutrients and also provide clues to understand the potential of methanogenesis.     

Diel Fluctuations in the Abundance and Community Diversity of Coastal Bacterioplankton Assemblages over a Tidal Cycle

The diel change in abundance and community diversity of the bacterioplankton assemblages within the Pacific Ocean at a fixed location in Monterey Bay, California (USA) were examined with several culture-independent (i.e., nucleic acid staining, fluorescence in situ hybridization {FISH}, and 16S ribosomal RNA gene libraries) approaches over a tidal cycle. FISH analyses revealed the quantitative predominance of bacterial members belonging to the Cytophaga-Flavobacterium cluster as well as two Proteobacteria (α- and γ-) subclasses within the bacterioplankton assemblages, especially during high tide (HT) and outgoing tide (OT) than the other tidal events. While the clone libraries showed that majority of the sequences were similar to the 16S rRNA gene sequences of unknown bacteria (32% to 73%), however, the operational taxonomic units from members of the α-Proteobacteria, Bacteroidetes, Firmicutes, and Cyanobacteria were also well represented during the four tidal events examined. Comparatively, sequence diversity was highest in OT, lowest in low tide, and very similar between HT and incoming tide. The results indicate that the dynamics of bacterial occurrence and diversity appeared to be more pronounced during HT and OT, further indicative of the ecological importance of several environmental variables including temperature, light intensity, and nutrient availability that are also concurrently fluctuating during these tidal events in marine systems.