Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution.

Cyanobacteria are recognised for their pivotal roles in aquatic ecosystems, serving as primary producers and major agents in diazotrophic processes. Currently, the primary focus of cyanobacterial research lies in gaining a more detailed understanding of these well-established ecosystem functions. However, their involvement and impact on other crucial biogeochemical cycles remain understudied. This knowledge gap is partially attributed to the challenges associated with culturing cyanobacteria in controlled laboratory conditions and the limited understanding of their specific growth requirements. This can be circumvented partially by the culture-independent methods which can shed light on the genomic potential of cyanobacterial species and answer more profound questions about the evolution of other key biogeochemical functions. In this study, we assembled 83 cyanobacterial genomes from metagenomic data generated from environmental DNA extracted from a brackish water lagoon (Chilika Lake, India). We taxonomically classified these metagenome-assembled genomes (MAGs) and found that about 92.77% of them are novel genomes at the species level. We then annotated these cyanobacterial MAGs for all the encoded functions using KEGG Orthology. Interestingly, we found two previously unreported functions in Cyanobacteria, namely, DNRA (Dissimilatory Nitrate Reduction to Ammonium) and DMSP (Dimethylsulfoniopropionate) synthesis in multiple MAGs using nirBD and dsyB genes as markers. We validated their presence in several publicly available cyanobacterial isolate genomes. Further, we identified incongruities between the evolutionary patterns of species and the marker genes and elucidated the underlying reasons for these discrepancies. This study expands our overall comprehension of the contribution of cyanobacteria to the biogeochemical cycling in coastal brackish ecosystems.

Co-occurrence patterns and environmental factors associated with rapid onset of Microcystis aeruginosa bloom in a tropical coastal lagoon.

The environmental factors contributing to the Microcystis aeruginosa bloom (hereafter referred to as Microcystis bloom) are still debatable as they vary with season and geographic settings. We examined the environmental factors that triggered Microcystis bloom outbreak in India's largest brackish water coastal lagoon, Chilika. The warmer water temperature (25.31-32.48 °C), higher dissolved inorganic nitrogen (DIN) loading (10.15-13.53 µmol L-1), strong P-limitation (N:P ratio 138.47-246.86), higher water transparency (46.62-73.38 cm), and low-salinity (5.45-9.15) exerted a strong positive influence on blooming process. During the bloom outbreak, M. aeruginosa proliferated, replaced diatoms, and constituted 70-88% of the total phytoplankton population. The abundances of M. aeruginosa increased from 0.89 × 104 cells L-1 in September to 1.85 × 104 cells L-1 in November and reduced drastically during bloom collapse (6.22 × 103 cells L-1) by the late November of year 2017. The decrease in M. aeruginosa during bloom collapse was associated with a decline in DIN loading (2.97 µmol L-1) and N:P ratio (73.95). Sentinel-3 OLCI-based satellite monitoring corroborated the field observations showing Cyanophyta Index (CI) > 0.01 in September, indicative of intense bloom and CI < 0.0001 during late November, suggesting bloom collapse. The presence of M. aeruginosa altered the phytoplankton community composition. Furthermore, co-occurrence network indicated that bloom resulted in a less stable community with low diversity, inter-connectedness, and prominence of a negative association between phytoplankton taxa. Variance partitioning analysis revealed that TSM (16.63%), salinity (6.99%), DIN (5.21%), and transparency (5.15%) were the most influential environmental factors controlling the phytoplankton composition. This study provides new insight into the phytoplankton co-occurrences and combination of environmental factors triggering the rapid onset of Microcystis bloom and influencing the phytoplankton composition dynamics of a large coastal lagoon. These findings would be valuable for future bloom forecast modeling and aid in the management of the lagoon.

Seagrasses and local environment control the bacterial community structure and carbon substrate utilization in brackish sediments.

Seagrasses are complex benthic coastal ecosystems that play a crucial role in organic matter cycling and carbon sequestration. However, little is known about how seagrasses influence the structure and carbon utilization potential of benthic bacterial communities. This study examined the bacterial communities in monospecific and mixed meadows of seagrasses and compared with bulk (unvegetated) sediments from Chilika, a brackish water coastal lagoon of India. High-throughput sequencing of 16S rRNA genes revealed a vegetation effect in terms of differences in benthic bacterial community diversity, composition, and abundances in comparison with bulk sediments. Desulfobacterales, Chromatiales, Enterobacteriales, Clostridiales, Vibrionales, and Acidimicrobiales were major taxa that contributed to differences between seagrass and bulk sediments. Seagrasses supported ∼5.94 fold higher bacterial abundances than the bulk due to rich organic carbon stock in their sediments. Co-occurrence network demonstrated much stronger potential interactions and connectedness in seagrass bacterial communities compared to bulk. Chromatiales and Acidimicrobiales were identified as the top two keystone taxa in seagrass bacterial communities, whereas, Dehalococcoidales and Rhizobiales were in bulk communities. Seagrasses and local environmental factors, namely, water depth, water pH, sediment salinity, redox potential, total organic carbon, available nitrogen, sediment texture, sediment pH, and sediment core depth were the major drivers of benthic bacterial community composition. Carbon metabolic profiling revealed that heterotrophic bacteria in seagrass sediments were much more metabolically diverse and active than bulk. The utilization of carbon substrate guilds, namely, amino acids, amines, carboxylic acids, carbohydrates, polymers, and phenolic compounds was enhanced in seagrass sediments. Metabolic mapping predicted higher prevalence of sulfate-reducer and N2 fixation metabolic functions in seagrass sediments. Overall, this study showed that seagrasses control benthic bacterial community composition and diversity, enhance heterotrophic carbon substrate utilization, and play crucial roles in organic matter cycling including degradation of hydrocarbon and xenobiotics in coastal sediments.

Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome.

Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.

Mangrovibacter phragmitis sp. nov., an endophyte isolated from the roots of Phragmites karka.

A facultatively anaerobic, Gram-stain-negative, rod-shaped, nitrogen-fixing, endophytic bacterial strain designated MP23T was isolated from the roots of Phragmites karka growing in Chilika Lagoon, Odisha, India. Strain MP23T was slightly halophilic, and the optimal NaCl concentration and temperature for growth were 1 % and 30 °C, respectively. On the basis of 16S rRNA gene sequence similarities, strain MP23T was affiliated to the family Enterobacteriaceae and most closely related to Mangrovibacter yixingensis KCTC 42181T and Mangrovibacter plantisponsor DSM 19579T with 99.71 % similarity, followed by Salmonella enterica subsp. salamae DSM 9220T (97.22 %), Cronobacter condimenti LMG 26250T (97.14 %) and Salmonella enterica subsp. diarizonae DSM 14847T (97 %). Sequence analysis of 16S rRNA, hsp60, gyrB and rpoB genes showed that strain MP23T formed a phylogenetic cluster with M. yixingensis KCTC 42181T and M. plantisponsor DSM 19579T indicating that it belongs to the genus Mangrovibacter. The major cellular fatty acids were C16 : 0, C18 : 1ω6c and/or C18 : 1ω7c, C16 : 1ω6c and/or C16 : 1ω7c, C14 : 0, C14 : 0 3-OH and/or iso-C16 : 1 I and C17 : 0 cyclo. Polar lipids of strain MP23T consisted of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 50.3 mol%. Based on experimental DNA-DNA hybridization values and average nucleotide identity derived from in silico comparison of whole-genome sequences, strain MP23T could be distinguished from its closest neighbours. We therefore conclude that strain MP23T represents a novel species of the genus Mangrovibacter for which the name Mangrovibacter phragmitis sp. nov. is proposed. The type strain is MP23T (=DSM 100250T=KCTC 42580T).

Streptomyces chitinivorans sp. nov., a chitinolytic strain isolated from estuarine lake sediment.

A novel actinobacterial strain RC1832T was isolated from the sediment of a fish dumping yard at Balugaon near Chilika Lake. The strain is halotolerant (15 % NaCl, w/v), alkali-tolerant (pH 7-10) and hydrolyzes chitin, starch, gelatin, cellulose, carboxymethyl cellulose, Tween 80, tributyrin, lecithin and casein. Apart from showing typical genus-specific morphological and chemotaxonomic features, the comparision and analysis of the near complete 16S rRNA gene sequence clearly revealed that the strain RC1832T represented a member of the genus Streptomyces. It exhibited the highest sequence similarities with the strains Streptomyces fenghuangensis GIMN4.003T (99.78 %), Streptomyces nanhaiensis DSM 41926T (99.07 %), Streptomyces radiopugnans R97T(98.71 %), Streptomyces atacamensis DSM 42065T (98.65 %) and Streptomyces barkulensis DSM 42082T (98.25 %). The DNA-DNA relatedness of strain RC 1832T with the closest phylogenetic neighbours S. fenghuangensis GIMN4.003T and S. nanhaiensis DSM 41926T were 20±2 % and 21±2 %, respectively. Thus, based on a range of phenotypic and genotypic properties, strain RC1832T was suggested to represent a novel species of the genus Streptomyces for which the name Streptomyces chitinivorans sp. nov. is proposed. The type strain is RC1832T (=JCM 30611=KCTC 29696).

Spatiotemporal distribution and composition of phytoplankton assemblages in a coastal tropical lagoon: Chilika, India.

The Asia's largest lagoon, Chilika, is a shallow water estuary and a designated "Ramsar" site located in the east coast of India. The spatiotemporal diversity of phytoplankton based on the monthly sampling between July 2011 and June 2012 was investigated in relation to physicochemical variables of the surface water column from 13 stations. The salinity was minimum (average 9) during the monsoon which was primarily due to riverine discharge. As the season progressed towards post-monsoon, average salinity of the whole lagoon reached to 10 which further increased to 20 during pre-monsoon season. A total of 259 species of phytoplankton, mostly dominated by the Bacillariophyta (138 species) followed by Dinophyta (38 species), Chlorophyta (32 species), Cyanophyta (29 species), Euglenophyta (18 species), and Chrysophyta (4 species), were recorded in this study. Different ecological sectors of the lagoon (except the northern sector) were dominated by diatoms, while the northern sector due to its freshwater regime supported large population of euglenoids. Based on the multivariate ordination analysis, salinity regime and light availability played important role in determining the distribution, diversity, and composition of phytoplankton communities. Overall, this study documented a very high diversity of phytoplankton and highlighted the importance of taking extensive sampling in getting a clearer understanding of phytoplankton community structure in less-studied environments such as Chilika lagoon.

Streptomyces barkulensis sp. nov., isolated from an estuarine lake.

The taxonomic position of a novel actinomycete, strain RC 1831(T), isolated from the sediment of a fish dumping yard at Barkul village near Chilika Lake, Odisha, India, was determined by a polyphasic approach. Based on morphological and chemotaxonomic characteristics the isolate was determined to belong to the genus Streptomyces. The phylogenetic tree based on its nearly complete 16S rRNA gene sequence (1428 nt) with representative strains showed that the strain consistently falls into a distinct phyletic line together with Streptomyces glaucosporus DSM 41689(T) (98.22% similarity) and a subclade consisting of Streptomyces atacamensis DSM 42065(T) (98.40%), Streptomyces radiopugnans R97 DSM 41901(T) (98.27%), Streptomyces fenghuangensis GIMN4.003(T) (98.33 %), Streptomyces nanhaiensis DSM 41926(T) (98.13%), Streptomyces megasporus NBRC 14749(T) (97.37%) and Streptomyces macrosporus NBRC 14748(T) (98.22%). However, the levels of DNA-DNA relatedness between strain RC 1831(T) and phylogenetically related strains Streptomyces atacamensis DSM 42065(T) (28.75 ± 3.25%) and Streptomyces glaucosporus DSM 41689(T) (15 ± 2.40%) were significantly lower than the 70% threshold value for delineation of genomic species. Furthermore, the isolate could be distinguished phenotypically on the basis of physiological, morphological and biochemical differences from its closest phylogenetic neighbours and other related reference strains. Strain RC 1831(T) is therefore considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces barkulensis sp. nov. is proposed. The type strain is RC 1831(T) ( = JCM 18754(T) = DSM 42082(T)).

Spatio-temporal structuring and assembly of abundant and rare bacteria in the benthic compartment of a marginally eutrophic lagoon.

The investigations on ecological processes that structure abundant and rare sub-communities are limited from the benthic compartments of tropical brackish lagoons. We examined the spatial and temporal patterns in benthic bacterial communities of a brackish lagoon; Chilika. Abundant and rare bacteria showed differences in niche specialization but exhibited similar distance-decay patterns. Abundant bacteria were mostly habitat generalists due to their broader niche breadth, environmental response thresholds, and greater functional redundancy. In contrast, rare bacteria were mostly habitat specialists due to their narrow niche breadth, lower environmental response thresholds, and functional redundancy. The spatial patterns in abundant bacteria were largely shaped by stochastic processes (88.7 %, mostly dispersal limitation). In contrast, rare bacteria were mostly structured by deterministic processes (56.4 %, mostly heterogeneous selection). These findings provided a quantitative assessment of the different forces namely spatial, environmental, and biotic that together structured bacterial communities in the benthic compartment of a marginally eutrophic lagoon.

Distinct community assembly processes and habitat specialization driving the biogeographic patterns of abundant and rare bacterioplankton in a brackish coastal lagoon.

The ecological diversity patterns and community assembly processes along spatio-temporal scales are least studied in the bacterioplankton sub-communities of brackish coastal lagoons. We examined the biogeographic patterns and relative influences of different assembly processes in structuring the abundant and rare bacterioplankton sub-communities of Chilika, the largest brackish water coastal lagoon of India. Rare taxa demonstrated significantly higher α- and ß-diversity and biogeochemical functions than abundant taxa in the high-throughput 16S rRNA gene sequence dataset. The majority of the abundant taxa (91.4 %) were habitat generalists with a wider niche breadth (niche breadth index, B = 11.5), whereas most of the rare taxa (95.2 %) were habitat specialists with a narrow niche breadth (B = 8.9). Abundant taxa exhibited a stronger distance-decay relationship and higher spatial turnover rate than rare taxa. ß-diversity partitioning revealed that the contribution of species turnover (72.2-97.8 %) was greater than nestedness (2.2-27.8 %) in causing the spatial variation in both abundant and rare taxa. Null model analyses revealed that the distribution of abundant taxa was mostly structured by stochastic processes (62.8 %), whereas deterministic processes (54.1 %) played a greater role in the rare taxa. However, the balance of these two processes varied across spatio-temporal scales in the lagoon. Salinity was the key deterministic factor controlling the variation of both abundant and rare taxa. Potential interaction networks showed a higher influence of negative interactions, indicating that species exclusion and top-down processes played a greater role in the community assembly. Notably, abundant taxa emerged as keystone taxa across spatio-temporal scales, suggesting their greater influences on other bacterial co-occurrences and network stability. Overall, this study provided detailed mechanistic insights into biogeographic patterns and underlying community assembly processes of the abundant and rare bacterioplankton over spatio-temporal scales in a brackish lagoon.

Investigation of microbial populations in the extremely metal-contaminated Coeur d'Alene River sediments.

The deposition of mine tailings generated from 125 years of sulfidic ore mining resulted in the enrichment of Coeur d'Alene River (CdAR) sediments with significant amounts of toxic heavy metals. A review of literature suggests that microbial populations play a pivotal role in the biogeochemical cycling of elements in such mining-impacted sedimentary environments. To assess the indigenous microbial communities associated with metal-enriched sediments of the CdAR, high-density 16S microarray (PhyloChip) and clone libraries specific to bacteria (16S rRNA), ammonia oxidizers (amoA), and methanogens (mcrA) were analyzed. PhyloChip analysis provided a comprehensive assessment of bacterial populations and detected the largest number of phylotypes in Proteobacteria followed by Firmicutes and Actinobacteria. Furthermore, PhyloChip and clone libraries displayed considerable metabolic diversity in indigenous microbial populations by capturing several chemolithotrophic groups such as ammonia oxidizers, iron-reducers and -oxidizers, methanogens, and sulfate-reducers in the CdAR sediments. Twenty-two phylotypes detected on PhyloChip could not be classified even at phylum level thus suggesting the presence of novel microbial populations in the CdAR sediments. Clone libraries demonstrated very limited diversity of ammonia oxidizers and methanogens in the CdAR sediments as evidenced by the fact that only Nitrosospira- and Methanosarcina-related phylotypes were retrieved in amoA and mcrA clone libraries, respectively.

Responses of phytoplankton community structure and association to variability in environmental drivers in a tropical coastal lagoon.

Spatial and seasonal heterogeneity in phytoplankton communities are governed by many biotic and abiotic drivers. However, the identification of long-term spatial and temporal trends in abiotic drivers, and their interdependencies with the phytoplankton communities' structure is understudied in tropical brackish coastal lagoons. We examined phytoplankton communities' spatiotemporal dynamics from a 5-year dataset (n = 780) collected from 13 sampling stations in Chilika Lagoon, India, where the salinity gradient defined the spatial patterns in environmental variables. Generalized additive models showed a declining trend in phytoplankton biomass, pH, and dissolved PO4 in the lagoon. Hierarchical modelling of species communities revealed that salinity (44.48 ± 28.19%), water temperature (4.37 ± 5.65%), and season (4.27 ± 0.96%) accounted for maximum variation in the phytoplankton composition. Bacillariophyta (Indicator Value (IV): 0.74) and Dinophyta (IV: 0.72) emerged as top indicators for polyhaline regime whereas, Cyanophyta (IV: 0.81), Euglenophyta (IV: 0.79), and Chlorophyta (IV: 0.75) were strong indicators for oligohaline regime. The responses of Dinophyta and Chrysophyta to environmental drivers were much more complex as random effects accounted for ~70-75% variation in their abundances. Prorocentrum minimum (IV: 0.52), Gonyaulax sp. (IV: 0.52), and Alexandrium sp. (IV: 0.51) were potential indicators of P-limitation. Diploneis weissflogii (IV: 0.43), a marine diatom, emerged as a potential indicator of N-limitation. Hierarchical modelling revealed the positive association between Cyanophyta, Chlorophyta, and Euglenophyta whereas, Dinophyta and Chrysophyta showed a negative association with Cyanophyta, Chlorophyta, and Euglenophyta. Landsat 8-Operational Land Imager satellite models predicted the highest and lowest Cyanophyta abundances in northern and southern sectors, respectively, which were in accordance with the near-coincident field-based measurements from the lagoon. This study highlighted the dynamics of phytoplankton communities and their relationships with environmental drivers by separating the signals of habitat filtering and biotic interactions in a monsoon-regulated tropical coastal lagoon.

Landfall season is critical to the impact of a cyclone on a monsoon-regulated tropical coastal lagoon.

Cyclones can produce a wide variety of short-term and long-term ecological impacts on coastal lagoons depending on cyclone's physical-meteorological characteristics and the lagoon's geographic, geomorphic, and bathymetric characteristics. Here, we theorized that in monsoon regulated tropical coastal lagoons, another important factor that could determine the impact of a cyclone is the landfall season or time of the year with reference to the monsoon season. We analyzed the impact of two cyclones which made landfall near Chilika, Asia's largest brackish water lagoon in different seasons, Cyclone Fani and Titli before and after the monsoon season. We compared field measured and satellite-derived water quality parameters including nutrient, salinity, water temperature, transparency, Chlorophyll-a (Chl-a), total suspended matter (TSM), and colored dissolved organic matter (CDOM) before and after the cyclones. We found that although both the cyclones were of similar intensities, after their land interaction, their impact on the lagoon's water quality was contrasting. The post-monsoon cyclone produced a substantial increase in total nitrogen (TN) and total phosphorous (TP), a large drop in salinity, CDOM, and Chl-a. In contrast, after the pre-monsoon cyclone, TN and TP did not show any such hike, no substantial change in salinity and CDOM either, and only a slight increase in Chl-a was observed. We found that the controlling factor in determining the impact of a cyclone is the rate and duration of freshwater discharge to the lagoon, which is normally a strong pulse for pre-monsoon and a continued high flow for post-monsoon cyclones. We conclude that the antecedent conditions of the lagoon and the watershed at the time of a cyclone's landfall is a key criterion in determining the impact. The combined use of satellite data and field data was proved critical to capture the overall impact of cyclones on the hydrological characteristics of the monsoon-regulated coastal lagoon.

Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library.

Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site.

Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake gold mine, South Dakota.

A microbial census on deep biosphere (1.34 km depth) microbial communities was performed in two soil samples collected from the Ross and number 6 Winze sites of the former Homestake gold mine, Lead, South Dakota using high-density 16S microarrays (PhyloChip). Soil mineralogical characterization was carried out using X-ray diffraction, X-ray photoelectron, and Mössbauer spectroscopic techniques which demonstrated silicates and iron minerals (phyllosilicates and clays) in both samples. Microarray data revealed extensive bacterial diversity in soils and detected the largest number of taxa in Proteobacteria phylum followed by Firmicutes and Actinobacteria. The archael communities in the deep gold mine environments were less diverse and belonged to phyla Euryarchaeota and Crenarchaeota. Both the samples showed remarkable similarities in microbial communities (1,360 common OTUs) despite distinct geochemical characteristics. Fifty-seven phylotypes could not be classified even at phylum level representing a hitherto unidentified diversity in deep biosphere. PhyloChip data also suggested considerable metabolic diversity by capturing several physiological groups such as sulfur-oxidizer, ammonia-oxidizers, iron-oxidizers, methane-oxidizers, and sulfate-reducers in both samples. High-density microarrays revealed the greatest prokaryotic diversity ever reported from deep subsurface habitat of gold mines.

The toxicity of lead to Desulfovibrio desulfuricans G20 in the presence of goethite and quartz.

An aqueous mixture of goethite, quartz, and lead chloride (PbCl(2)) was treated with the sulfate-reducing bacterium, Desulfovibrio desulfuricans G20 (D. desulfuricans G20), in a medium specifically designed to assess metal toxicity. In the presence of 26 muM of soluble Pb, together with the goethite and quartz, D. desulfuricans G20 grew after a lag time of 5 days compared to 2 days in Pb-, goethite-, and quartz-free treatments. In the absence of goethite and quartz, however, with 26 microM soluble Pb, no measurable growth was observed. Results showed that D. desulfuricans G20 first removed Pb from solutions then growth began resulting in black precipitates of Pb and iron sulfides. Transmission electron microscopic analyses of thin sections of D. desulfuricans G20 treated with 10 microM PbCl(2) in goethite- and quartz-free treatment showed the presence of a dense deposit of lead sulfide precipitates both in the periplasm and cytoplasm. However, thin sections of D. desulfuricans G20 treated with goethite, quartz, and PbCl(2) (26 microM soluble Pb) showed the presence of a dense deposit of iron sulfide precipitates both in the periplasm and cytoplasm. Energy-dispersive X-ray spectroscopy, selected area electron diffraction patterns, or X-ray diffraction analyses confirmed the structure of precipitated Pb inside the cell as galena (PbS) in goethite- and quartz-free treatments, and iron sulfides in treatments with goethite, quartz, and PbCl(2). Overall results suggest that even at the same soluble Pb concentration (26 microM), in the presence of goethite and quartz, apparent Pb toxicity to D. desulfuricans G20 decreased significantly. Further, accumulation of lead/iron sulfides inside D. desulfuricans G20 cells depended on the presence of goethite and quartz.

Benthic archaeal community structure and carbon metabolic profiling of heterotrophic microbial communities in brackish sediments.

Benthic Archaea play a crucial role in the biogeochemical cycles and food webs, however, their spatiotemporal distribution and environmental drivers are not well investigated in brackish sediments. The composition and abundances of benthic archaeal communities were examined from a coastal lagoon; Chilika (India) which is experiencing an intense pressure from anthropogenic and natural factors. High-throughput sequencing of 16S rRNA genes revealed that sediment (n = 96) archaeal communities were largely composed of Crenarchaeota (18.76%), Euryarchaeota (18.34%), Thaumarchaeota (13.45%), Woesearchaeota (10.05%), and Pacearchaeota (4.21%). Archaeal taxa affiliated to methanogens, sulfate-reducers, and ammonia-oxidizers were detected suggesting that carbon, sulfur, and nitrogen cycles might be prominent in benthic sediments. Salinity, total organic carbon, available nitrogen, available phosphorus, macrophyte (Phragmites karka) and inter-taxa relationships between community members and with bacterial communities played steering roles in structuring the archaeal communities. Marine sites with mesohaline-polyhaline regime were dominated by Nitrosopumilus and Thaumarchaeota. In contrast, riverine sites with oligohaline regime demonstrated a higher abundance of Thermoprotei. Macrophyte dominated zones were enriched in Methanomicrobia and Methanobacteria in their rhizosphere sediments, whereas, bulk (un-vegetated) sediments were dominated by Nitrosopumilus. Spatial patterns in archaeal communities demonstrated 'distance-decay' patterns which were correlated with changes in physicochemical factors over geographical distances. Heterotrophic microbial communities showed much higher metabolic diversity and activity in their carbon utilization profiles in rhizosphere sediments than the bulk sediments. This baseline information on benthic archaea and their environmental drivers would be useful to assess the impact of anthropogenic and natural pressures on these communities and associated biogeochemical cycles.

Seasonal and spatial dynamics of bacterioplankton communities in a brackish water coastal lagoon.

Coastal ecosystems, one of the most productive ecosystems, are subjected to natural and anthropogenic stresses. Coastal bacterioplankton communities are highly dynamic due to spatiotemporal heterogeneity in the environmental parameters. We investigated the seasonal and spatial variation in bacterioplankton communities, their abundances and environmental drivers during one year period in Chilika, a brackish water coastal lagoon of India. High-throughput sequencing of 16S rRNA genes of bacterioplankton communities showed that they were dominated by heterotrophs namely α-Proteobacteria SAR11 and their sub-clades (SAR11_Ib, Chesapeake-Delaware_Bay, Candidatus_Pelagibacter, and SAR11_Surface_1), actinobacterial lineages (hgcI, CL500-29, and Candidatus_Aquiluna), ß-Proteobacteria MWH-UniP1, ß-Proteobacteria OM43, and verrucomicrobial clade Spartobacteria 'LD29'. Synechococcus was the dominant member within autotrophic cyanobacterial community. Response ratio derived from comparisons of taxon-specific absolute abundances and indicator analyses showed that SAR11_Surface_1 sub-clade occupied high-salinity environment especially during summer and winter and emerged as a strong indicator for mesohaline-polyhaline salinity regime. In contrast, Spartobacteria 'LD29', Actinobacteria hgcI, and CL500-29 preferred low-salinity freshwater environment and were strong indicators for oligohaline-mesohaline regimes. Spatiotemporal patterns were governed by 'distance-decay' and 'similarity-time' relationships. Bacterioplankton communities were mostly determined by salinity, dissolved oxygen, phosphate, and pH which resulted 'species sorting' leading to biogeographical patterns in the bacterioplankton communities. Modeling analysis revealed the characteristic shift in the indicator bacterioplankton taxa along with estuarine salinity gradient. This study has provided baseline information on the bacterioplankton communities and their environmental drivers within an anthropogenically impacted cyclone prone coastal lagoon which would be useful in assessing the impact of multiple stressors on this vulnerable ecosystem.

Molecular studies on the microbial diversity associated with mining-impacted Coeur d'Alene River sediments.

The prokaryotic diversity associated with highly metal-contaminated sediment samples collected from the Coeur d'Alene River (CdAR) was investigated using a cultivation-independent approach. Bacterial community structure was studied by constructing an RNA polymerase beta subunit (rpoB) gene library. Phylogenetic analysis revealed that 75.8% of the rpoB clones were associated with beta-Proteobacteria while the remaining 24.2% were with gamma-Proteobacteria. All phylotypes showed close similarity to previously reported cultivable lineages from metal or organic contaminant-rich environments. In an archaeal 16S rRNA gene library, 70% of the clones were affiliated to Crenarchaeota, while 30% belonged to Euryarchaeota. Most of the Euryarchaeota sequences were related to acetoclastic lineages belonging to Methanosarcinales. A single phylotype within the Euryarchaeota showed no association with cultivable euryarchaeotal lineages and might represent novel taxon. Diversity indices demonstrated greater diversity of Bacteria compared to Archaea in CdAR sediments. Sediment characterization by the X-ray fluorescence spectroscopy revealed high amount of toxic metals. To our knowledge, this is the first culture-independent survey on the prokaryotic diversity present in mining-impacted sediments of CdAR.

Isolation and characterization of cellulose-degrading bacteria from the deep subsurface of the Homestake gold mine, Lead, South Dakota, USA.

The present study investigated the cultivable mesophilic (37 degrees C) and thermophilic (60 degrees C) cellulose-degrading bacterial diversity in a weathered soil-like sample collected from the deep subsurface (1.5 km depth) of the Homestake gold mine in Lead, South Dakota, USA. Chemical characterization of the sample by X-ray fluorescence spectroscopy revealed a high amount of toxic heavy metals such as Cu, Cr, Pb, Ni, and Zn. Molecular community structures were determined by phylogenetic analysis of 16S rRNA gene sequences retrieved from enrichment cultures growing in presence of microcrystalline cellulose as the sole source of carbon. All phylotypes retrieved from enrichment cultures were affiliated to Firmicutes. Cellulose-degrading mesophilic and thermophilic pure cultures belonging to the genera Brevibacillus, Paenibacillus, Bacillus, and Geobacillus were isolated from enrichment cultures, and selected cultures were studied for enzyme activities. For a mesophilic isolate (DUSELG12), the optimum pH and temperature for carboxymethyl cellulase (CMCase) were 5.5 and 55 degrees C, while for a thermophilic isolate (DUSELR7) they were 5.0 and 75 degrees C, respectively. Furthermore, DUSELG12 retained about 40% CMCase activity after incubation at 60 degrees C for 8 h. Most remarkably, thermophilic isolate, DUSELR7 retained 26% CMCase activity at 60 degrees C up to a period of 300 h. Overall, the present work revealed the presence of different cellulose-degrading bacterial lineages in the unique deep subsurface environment of the mine. The results also have strong implications for biological conversion of cellulosic agricultural and forestry wastes to commodity chemicals including sugars.