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 ß-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.

An index for discrimination of mangroves from non-mangroves using LANDSAT 8 OLI imagery.

Over the last few decades several vegetation indices were used to map Mangrove forest using satellite images. Difficulty still persists in discrimination of mangroves from non-mangrove vegetation, especially in areas where mangrove species are mixed with other vegetation types. In the present study we have attempted to develop an improved index, which utilizes the information from the Normalized Difference Vegetation Index (NDVI) and the Normalized Difference Water Index (NDWI) of Bhitarkanika mangrove forest of Odisha, India. These indices are negatively correlated (r = -0.988; p < 0.01). Further, the NDWI values were subtracted from the NDVI values at the pixel level. As the outputs are negatively related, subtraction increases the upper and lower range of the overall output, also increasing the distinct values of two classes with near-similar spectral signatures. Same algorithm was applied on mangroves of Sundarbans (r = -0.987) and Andaman (r = -0.989). A comparison between four established indices [NDVI, NDWI, Soil Adjusted Vegetation Index (SAVI), Simple Ratio (SR)] and the newly developed index namely Combined Mangrove Recognition Index (CMRI) were performed. Accuracy assessment using Kappa statistics, revealing that CMRI produces better accuracy (73.43%) compared to other indices, followed by NDVI (56.29%) and SR (48.79%).

Taxonomic description and draft genome of Pseudomonas sediminis sp. nov., isolated from the rhizospheric sediment of Phragmites karka.

The taxonomic position of a Gram-stain-negative, rod-shaped bacterial strain, designated PI11T, isolated from the rhizospheric sediment of Phragmites karka was characterized using a polyphasic approach. Strain PI11T could grow optimally at 1.0% NaCl concentration with pH 7.0 at 30°C and was positive for oxidase and catalase but negative for hydrolysis of starch, casein, and esculin ferric citrate. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain PI11T belonged to the genus Pseudomonas sharing the highest sequence similarities with Pseudomonas indoloxydans JCM 14246T (99.72%), followed by, Pseudomonas oleovorans subsp. oleovorans DSM 1045T (99.29%), Pseudomonas toyotomiensis JCM 15604T (99.15%), Pseudomonas chengduensis DSM 26382T (99.08%), Pseudomonas oleovorans subsp. lubricantis DSM 21016T (99.08%), and Pseudomonas alcaliphila JCM 10630T (99.01%). Experimental DNA-DNA relatedness between strain PI11T and P. indoloxydans JCM 14246T was 49.4%. The draft genome of strain PI11T consisted of 4,884,839 bp. Average nucleotide identity between the genome of strain PI11T and other closely related type strains ranged between 77.25-90.74%. The polar lipid pattern comprised of phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major (> 10%) cellular fatty acids were C18:1ω6c/ω7c, C16:1ω6c/ω7c, and C16:0. The DNA G + C content of strain PI11T was 62.4 mol%. Based on the results of polyphasic analysis, strain PI11T was delineated from other closely related type strains. It is proposed that strain PI11T represents represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sediminis sp. nov. is proposed. The type strain is PI11T (= KCTC 42576T = DSMZ 100245T).

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 ß-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.

Sources and Variability of Petroleum Hydrocarbon Residues in Sediments of Chilika Lagoon, East Coast of India.

The spatio-temporal distribution and the controlling factors of petroleum hydrocarbons (PHCs) in sediments of Chilika lagoon was investigated. Samples were collected during three seasons and quantified using UV-fluorescence spectroscopy. Concentrations of PHCs in surface sediments varies from 0.18 to 12.13 ppm (mean 3.71 ± 3.94 ppm). Compared to the lagoon, the monitoring stations adjacent to jetties with high boating activities tend to have higher PHC concentrations, suggesting that the contribution is likely to be from fossil fuel combustion and accidental seepage. The sediment organic matter (OM) of Chilika ranges from 0.26% to 6.23%. PHC maintains a positive correlation with OM (p < 0.05; f = 0.334), indicating the long term deposition of PHC as sediment OM. However, there is no significant relation between PHC and sediment texture, indicating its negligible control over PHC. The recorded PHC concentrations are below the threshold limit (70 ppm) as classified by United States (US) National Academy of Sciences (NAS) and also lower than those reported from similar ecosystems in India and overseas. Since the long term deposition and the bioaccumulation of PHC cannot be avoided, it is essential to monitor these parameters periodically.

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).

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.

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.