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.

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 β-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. β-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.

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.

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.

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.

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.

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), β-Proteobacteria MWH-UniP1, β-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.

Spatial and temporal heterogeneity in the structure and function of sediment bacterial communities of a tropical mangrove forest

Bacterial communities of mangrove sediments are well appreciated for their role in nutrient cycling. However, spatiotemporal variability in these communities over large geographical scale remains understudied. We investigated sediment bacterial communities and their metabolic potential in an intertidal mangrove forest of India, Bhitarkanika, using high-throughput sequencing of 16S rRNA genes and community-level physiological profiling. Bulk surface sediments from five different locations representing riverine and bay sites were collected over three seasons. Seasonality largely explained the variation in the structural and metabolic patterns of the sediment bacterial communities. Freshwater Actinobacteria were more abundant in monsoon, whereas γ-Proteobacteria demonstrated higher abundance in summer. Distinct differences in the bacterial community composition were noted between riverine and bay sites. For example, salt-loving marine bacteria affiliated to Oceanospirillales were more prominent in the bay sites than the riverine sites. L-asparagine, N-acetyl-D-glucosamine, and D-mannitol were the preferentially utilized carbon sources by bacterial communities. Bacterial community composition was largely governed by salinity and organic carbon content of the sediments. Modeling analysis revealed that the abundance of δ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed an opposite trend. Metabolic mapping of taxonomic data predicted biogeochemical functions such as xylan and chitin degradation, ammonia oxidation, nitrite reduction, and sulfate reduction in the bacterial communities suggesting their role in carbon, nitrogen, and sulfur cycling in mangrove sediments. This study has provided valuable clues about spatiotemporal heterogeneity in the structural and metabolic patterns of bacterial communities and their environmental determinants in a tropical mangrove forest.

Taxonomic description and genome sequence of Halobacillus marinus sp. nov., a novel strain isolated from Chilika Lake, India

moderately halophilic spore forming, motile, Gram-positive, rod-shaped bacterial strain designated as KGW1^T was isolated from water sample of Chilika Lake and characterized taxonomically using polyphasic approach. The strain grew in the presence of 0-25% (w/v) NaCl in marine salt agar media, hydrolyzes casein, and gelatin and shows presence of alkaline proteases. The major cell wall menaquinone was MK7 and major cellular fatty acids were anteiso-C_15:0 (44.89%), anteiso-C_17:0 (6.18%), isoC_15:0 (19.38%), and iso-C_16:0 (7.39%). Several chemotaxonomic features conform the isolate be a member of genus Halobacillus. The isolate KGW1^T contained A1γ meso-Dpm-direct type of peptidoglycan which is different from its phylogenetically closest neighbours. The 16S rRNA gene sequence based phylogenetic analysis also revealed the strain KGW1^T was affiliated to the genus Halobacillus and sequence similarity between the isolated strain and the type strains of Halobacillus species were found closest to, H. dabanensis D-8 DSM 18199^T (99.08%) and H. faecis IGA7-4 DSM 21559^T (99.01%), H. trueperi SL-5 DSM 10404^T (98.94%). The in silico DDH showed that the values in a range of 14.2-17.5% with the most closest strain H. dabanensis D-8 DSM 18199^T and other type strains of the genus Halobacillus for which whole genome sequence is reported. DNA-DNA relatedness between strain KGW1^T and the closest type strain Halobacillus trueperi DSM 10404^T was 11.75% (± 1.15). The draft genome sequence includes 3,683,819 bases and comprises of 3898 predicted coding sequences with a G + C content of 46.98%. Thus, the significant distinctiveness supported by phenotypic and genotypic data with its closest neighbors and other closely related species confirm the strain KGW1^T to be classified as a novel species within the genus Halobacillus, for which the name Halobacillus marinus sp. nov. is proposed. The type strain is KGW1^T (= DSM 29522 = JCM 30443).

Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon

Brackish water coastal lagoons are least understood with respect to the seasonal and temporal variability in their sedimentary bacterial communities. These coastal lagoons are characterized by the steep environmental gradient and provide an excellent model system to decipher the biotic and abiotic factors that determine the bacterial community structure over time and space. Using Illumina sequencing of the 16S rRNA genes from a total of 100 bulk surface sediments, we investigated the sedimentary bacterial communities, their spatiotemporal distribution, and compared them with the rhizosphere sediment communities of a common reed; Phragmites karka and a native seagrass species; Halodule uninervis in Chilika Lagoon. Spatiotemporal patterns in bacterial communities were linked to specific biotic factors (e.g., presence and type of macrophyte) and abiotic factors (e.g., salinity) that drove the community composition. Comparative assessment of communities highlighted bacterial lineages that were responsible for segregating the sediment communities over distinct salinity regimes, seasons, locations, and presence and type of macrophytes. Several bacterial taxa were specific to one of these ecological factors suggesting that species-sorting processes drive specific biogeographical patterns in the bacterial populations. Modeling of proteobacterial lineages against salinity gradient revealed that α- and γ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed the opposite trend. The wide variety of biogeochemical functions performed by the rhizosphere microbiota of P. karka must be taken into consideration while formulating the management and conservation plan for this reed. Overall, this study provides a comprehensive understanding of the spatiotemporal dynamics and functionality of sedimentary bacterial communities and highlighted the role of biotic and abiotic factors in generating the biogeographical patterns in the bacterial communities of a tropical brackish water coastal lagoon.

The draft genome sequence of Mangrovibacter sp. strain MP23, an endophyte isolated from the roots of Phragmites karka

Till date, only one draft genome has been reported within the genus Mangrovibacter. Here, we report the second draft genome shotgun sequence of a Mangrovibacter sp. strain MP23 that was isolated from the roots of Phargmites karka (P. karka), an invasive weed growing in the Chilika Lagoon, Odisha, India. Strain MP23 is a facultative anaerobic, nitrogen-fixing endophytic bacteria that grows optimally at 37 °C, 7.0 pH, and 1% NaCl concentration. The draft genome sequence of strain MP23 contains 4,947,475 bp with an estimated G + C content of 49.9% and total 4392 protein coding genes. The genome sequence has provided information on putative genes that code for proteins involved in oxidative stress, uptake of nutrients, and nitrogen fixation that might offer niche specific ecological fitness and explain the invasive success of P. karka in Chilika Lagoon. The draft genome sequence and annotation have been deposited at DDBJ/EMBL/GenBank under the accession number LYRP00000000.

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).

Interannual and cyclone-driven variability in phytoplankton communities of a tropical coastal lagoon

One of the main challenges in phytoplankton ecology is to understand their variability at different spatiotemporal scales. We investigated the interannual and cyclone-derived variability in phytoplankton communities of Chilika, the largest tropical coastal lagoon in Asia and the underlying mechanisms in relation to environmental forcing. Between July 2012 and June 2013, Cyanophyta were most prolific in freshwater northern region of the lagoon. A category-5 very severe cyclonic storm (VSCS) Phailin struck the lagoon on 12th October 2013 and introduced additional variability into the hydrology and phytoplankton communities. Freshwater Cyanophyta further expanded their territory and occupied the northern as well as central region of the lagoon. Satellite remote sensing imagery revealed that the phytoplankton biomass did not change much due to high turbidity prevailing in the lagoon after Phailin. Modeling analysis of species-salinity relationship identified specific responses of phytoplankton taxa to the different salinity regime of lagoon.

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.

Molecular phylogenetic profiling of gut-associated bacteria in larvae and adults of flesh flies

Flesh flies of the genus Sarcophaga (Diptera: Sarcophagidae) are carrion-breeding, necrophagous insects important in medical and veterinary entomology as potential transmitters of pathogens to humans and animals. Our aim was to analyse the diversity of gut-associated bacteria in wild-caught larvae and adult flesh flies using culture-dependent and culture-independent methods. Analysis of 16S rRNA gene sequences from cultured isolates and clone libraries revealed bacteria affiliated to Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes in the guts of larval and adult flesh flies. Bacteria cultured from larval and adult flesh fly guts belonged to the genera Acinetobacter, Bacillus, Budvicia, Citrobacter, Dermacoccus, Enterococcus, Ignatzschineria, Lysinibacillus, Myroides, Pasteurella, Proteus, Providencia and Staphylococcus. Phylogenetic analysis showed clone sequences of the genera Aeromonas, Bacillus, Bradyrhizobium, Citrobacter, Clostridium, Corynebacterium, Ignatzschineria, Klebsiella, Pantoea, Propionibacterium, Proteus, Providencia, Serratia, Sporosarcina, Weissella and Wohlfahrtiimonas. Species of clinically significant genera such as Ignatzschineria and Wohlfahrtiimonas spp. were detected in both larvae and adult flesh flies. Sequence analysis of 16S rRNA gene libraries supported culture-based results and revealed the presence of additional bacterial taxa. This study determined the diversity of gut microbiota in flesh flies, which will bolster the ability to assess microbiological risk associated with the presence of these flies. The present data thereby establish a platform for a much larger study.

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

The taxonomic position of a novel actinomycete, strain RC 1831T, 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 41689T (98.22 % similarity) and a subclade consisting of Streptomyces atacamensis DSM 42065T (98.40 %), Streptomyces radiopugnans R97 DSM 41901T (98.27 %), Streptomyces fenghuangensis GIMN4.003T (98.33 %), Streptomyces nanhaiensis DSM 41926T (98.13 %), Streptomyces megasporus NBRC 14749T (97.37 %) and Streptomyces macrosporus NBRC 14748T (98.22 %). However, the levels of DNA–DNA relatedness between strain RC 1831T and phylogenetically related strains Streptomyces atacamensis DSM 42065T (28.75±3.25 %) and Streptomyces glaucosporus DSM 41689T (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 1831T 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 1831T ( = JCM 18754T = DSM 42082T).

Presence of glucose, xylose, and glycerol fermenting bacteria in the deep biosphere of the former Homestake gold mine, South Dakota

Eight fermentative bacterial strains were isolated from mixed enrichment cultures of a composite soil sample collected at 1.34 km depth from the former Homestake gold mine in Lead, SD, USA. Phylogenetic analysis of their 16S rRNA gene sequences revealed that these isolates were affiliated with the phylum Firmicutes belonging to genera Bacillus and Clostridium. Batch fermentation studies demonstrated that isolates had the ability to ferment glucose, xylose, or glycerol to industrially valuable products such as ethanol and 1,3-propanediol (PDO). Ethanol was detected as the major fermentation end product in glucose-fermenting cultures at pH 10 with yields of 0.205–0.304 g of ethanol/g of glucose. While a xylose-fermenting strain yielded 0.189 g of ethanol/g of xylose and 0.585 g of acetic acid/g of xylose at the end of fermentation. At pH 7, glycerol-fermenting isolates produced PDO (0.323–0.458 g of PDO/g of glycerol) and ethanol (0.284–0.350 g of ethanol/g of glycerol) as major end products while acetic acid and succinic acid were identified as minor by-products in fermentation broths. These results suggest that the deep biosphere of the former Homestake gold mine harbors bacterial strains which could be used in bio-based production of ethanol and PDO.

Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce

The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009-2010 crop cycle. Total bacterial populations averaged between 10(5) and 10(6) per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial 'core' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment.

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.

Characterization of thermostable cellulases produced by Bacillus and Geobacillus strains

The composition of thermophilic (60 degrees C) mixed cellulose-degrading enrichment culture initiated from compost samples was examined by constructing a 16S rRNA gene clone library and the presence of sequences related to Actinobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Proteobacteria were identified. Eight isolates capable of degrading cellulose, carboxymethyl cellulose (CMC), or ponderosa pine sawdust were identified as belonging to the genera Geobacillus, Thermobacillus, Cohnella, and Thermus. A compost isolate WSUCF1 (Geobacillus sp.) was selected based on its higher growth rate and cellulase activity compared to others in liquid minimal medium containing cellulose as a source of carbon and energy. Strain WSUCF1 and a previously isolated thermophilic cellulose-degrading deep gold mine strain DUSELR13 (Bacillus sp.) were examined for their enzyme properties and kinetics. The optimal pH for carboxymethyl cellulase (CMCase) activity was 5.0 for both isolates. The optimum temperatures for CMCase of WSUCFI and DUSELR13 were 70 and 75 degrees C, respectively. For CMC, the DUSELR13 and WSUCF1 CMCases had K(m) values of 3.11 and 1.08mg/ml, respectively. Most remarkably, WSUCF1 and DUSELR13 retained 89% and 78% of the initial CMCase activities, respectively, after incubation at 70 degrees C for 1day. These thermostable enzymes would facilitate development of more efficient and cost-effective forms of the simultaneous saccharification and fermentation process to convert lignocellulosic biomass into biofuels.

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.

A PCR-based toolbox for the culture-independent quantification of total bacterial abundances in plant environments

A major obstacle in the culture-independent estimation of the abundance of bacteria associated with plants is contamination with plant organelles, which precludes the use of universal rRNA bacterial primers in quantitative PCR applications. We present here a PCR-based method that allows a priori determination of the degree of chloroplast and mitochondrial contamination in DNA samples from plant environments. It is based on differential digestibility of chloroplast, mitochondrial and bacterial small subunit rRNA gene amplicons with the restriction enzymes AfeI and BbvCI. Using this method, we demonstrated for field-grown lettuce plants that even a gentle washing protocol, designed to recover the microbial community and its metagenome from the leaf surface, resulted in substantial contamination with chloroplast DNA. This finding cautions against the use of universal primer pairs that do not exclude chloroplast DNA from amplification, because they risk overestimation of bacterial population sizes. In contrast, contamination with mitochondrial 18S rRNA was minor in the lettuce phyllosphere. These findings were confirmed by real-time PCR using primer sets specific for small subunit rRNA genes from bacteria, chloroplasts, and mitochondria. Based on these results, we propose two primer pairs (534f/783r and mito1345f/mito1430r) which between them offer an indirect means of faithfully estimating bacterial abundances on plants, by deduction of the mito1345f/mito1430r-based mitochondrial count from that obtained with 534f/783r, which amplifies both bacterial and mitochondrial DNA but excludes chloroplast. In this manner, we estimated the number of total bacteria on most leaves of field-grown lettuce to be between 10(5) and 10(6) g(-1) of leaf, which was 1-3 orders of magnitudes higher than the number of colony-forming units that were retrieved from the same leaf surfaces on agar plates.

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.

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.

Molecular analysis of prokaryotic diversity in the deep subsurface of the former Homestake gold mine, South Dakota, USA

A culture-independent molecular phylogenetic analysis was carried out to study the prokaryotic diversity in two soil samples collected from the subsurface (1.34 km depth) of the former Homestake gold mine, Lead, South Dakota, USA at two sites, the Ross shaft and number 6 Winze. Microbial community analyses were performed by cloning and sequencing of 16S rRNA genes retrieved directly from soil samples. Geochemical characterization of soils revealed high amount of toxic metals such as As, Cd, Co, Cr, Cu, Ni, Pb, Zn, and U at both the sites. Phylogenetic analyses showed that soil samples were predominantly composed of phylotypes related to phylum Proteobacteria. Other phyla detected in libraries were Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Verrucomicrobia, and candidate divisions OP10 and TM7. The majority (>95%) of the phylotypes retrieved in the libraries were most closely related to environmental sequences from yet-uncultured bacteria representing a hitherto unidentified diversity. The archaeal communities at both the sites exhibited lower diversity and were most closely affiliated to uncultivated species within the Crenarchaeota. Results showed the existence of diverse microbial populations in deep subsurface environment of the Homestake gold mine. Statistical analyses demonstrated that each site harbored phylogenetically distinct microbial populations that were more diverse at Ross site compare to winze site.

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.

Investigation of methanogen population structure in biogas reactor by molecular characterization of methyl-coenzyme M reductase A (mcrA) genes

The methanogen community in biogas reactor running on cattle dung was investigated in two different seasons; summer (April, 36 degrees C) and winter (December, 24 degrees C), in the year 2004 by a culture-independent approach. Community structure was determined by phylogenetic analyses of 343 and 278 mcrA clones belonging to summer and winter month libraries, respectively. In summer month's library, 41.7% clones were affiliated to Methanomicrobiales, 30% to Methanosarcinales, 19% to Methanobacteriales, 5% to Methanococcales and a total of 4.3% clones belonged to unclassified euryarchaeotal lineages. In winter month's library, Methanomicrobiales encompassed 98.6% clones, and Methanobacteriales included 1.4% of total clone diversity. Biogas plant performance data collected during the winter month indicated significant reduction in daily biogas produced as compared to summer month because of lowering in ambient temperature and associated shift in microbial community. Results from this molecular study showed the existence of highly diverse and complex methanogens communities present in biogas plant.

Novel methanotroph diversity evidenced by molecular characterization of particulate methane monooxygenase A (pmoA) genes in a biogas reactor

The present study for the first time investigated the diversity of methanotrophs in a biogas reactor running on cattle dung by sequence analysis of the "functional" gene, particulate methane monooxygenase A (pmoA). Community structure was determined by operational taxonomic unit (OTU) phylogenetic analyses of 396 clones belonging to pmoA library. On the basis of 95% peptide identity, 396 inferred PmoA peptide sequences were clustered in 22 phylotypes. These OTUS were phylogenetically affiliated to alpha-proteobacteria (5.30% clones) and gamma-proteobacteria (94.7% clones) and were only distantly related to those of known methanotrophs, indicating the existence of unknown methanotrophs involved in aerobic methanotrophy inside the biogas plant. Good's coverage indicated that the present library covered 96.21% of the dominant species that could be cloned from the biogas reactor. The molecular approaches used in this study provided useful description of the microbial community involved in aerobic oxidation of methane.

Isolation and characterization of a new osmotolerant, non-virulent Klebsiella pneumoniae strain SAP for biosynthesis of succinic acid

In the present study, isolation of anaerobic bacteria from 24 different eco-niches was carried out. A total number of 300 bacterial isolates, including 230 obligate and 70 facultative anaerobes were obtained using anaerobic techniques. All the isolates were initially screened for succinic acid production by Fluorescein test and TLC method. During screening, 10 isolates found to produce succinic acid were further examined by HPLC and then finally confirmed for succinic acid by LC-MS analysis. Amongst 10 isolates, isolate SAP, a facultative anaerobe isolated from buffalo rumen fluid, showed maximum yield of 2.1 g/l of succinic acid from 10 g of glucose in 24 hr under anaerobic condition. This isolate was identified as Klebsiella pneumoniae strain SAP by 16S rDNA sequence and signature sequence analysis. Mouse lethality test for the strain SAP showed LD50 value of 3.3 x 10(8) CFU/ml, which shows non-virulent nature of the strain. This strain may become a candidate strain for succinic acid production because of its osmotolerant nature and higher succinate:acetate ratio.