Insights on aquatic microbiome of the Indian Sundarbans mangrove areas

Background: Anthropogenic perturbations have strong impact on water quality and ecological health of mangrove areas of Indian Sundarbans. Diversity in microbial community composition is important causes for maintaining the health of the mangrove ecosystem. However, microbial communities of estuarine water in Indian Sundarbans mangrove areas and environmental determinants that contribute to those communities were seldom studied. Methods: Nevertheless, this study attempted first to report bacterial and archaeal communities simultaneously in the water from Matla River and Thakuran River of Maipith coastal areas more accurately using 16S rRNA gene-based amplicon approaches. Attempt also been made to assess the capability of the environmental parameters for explaining the variation in microbial community composition. Results: Our investigation indicates the dominancy of halophilic marine bacteria from families Flavobacteriaceae and OM1 clade in the water with lower nutrient load collected from costal regions of a small Island of Sundarban Mangroves (ISM). At higher eutrophic conditions, changes in bacterial communities in Open Marine Water (OMW) were detected, where some of the marine hydrocarbons degrading bacteria under families Oceanospirillaceae and Spongiibacteraceae were dominated. While most abundant bacterial family Rhodobacteracea almost equally (18% of the total community) dominated in both sites. Minor variation in the composition of archaeal community was also observed between OMW and ISM. Redundancy analysis indicates a combination of total nitrogen and dissolved inorganic nutrients for OMW and for ISM, salinity and total nitrogen was responsible for explaining the changes in their respective microbial community composition. Conclusions: Our study contributes the first conclusive overview on how do multiple environmental/ anthropogenic stressors (salinity, pollution, eutrophication, land-use) affect the Sundarban estuary water and consequently the microbial communities in concert. However, systematic approaches with more samples for evaluating the effect of environmental pollutions on mangrove microbial communities are recommended.Fil: Dhal, Paltu Kumar. Jadavpur University; IndiaFil: Kopprio, Germán Adolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentina. Leibniz Center for Tropical Marine Research; AlemaniaFil: Gärdes, Astrid. Leibniz Center for Tropical Marine Research; Alemani

Structure and co-occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacific white-leg shrimp Penaeus vannamei aquaculture

Bacterial diseases cause production failures in shrimp aquacultures.to understand environmental conditions and bacterial community dynamics contributing to white faeces disease (WFD) events, we analysed water quality and compared bacterial communities in water as well as in intestines and faeces of healthy and diseased shrimps, respectively, via 16S rRNA gene sequencing and qPCR of transmembrane regulatory protein (toxR), thermolabile haemolysin (tlh), and thermostable direct haemolysin genes of pathogenic Vibrio parahaemolyticus as a proxy for virulence. WfD occurred when pH decreased to 7.71–7.84, and Alteromonas, Pseudoalteromonas and Vibrio dominated the aquatic bacterial communities. the disease severity further correlated with increased proportions of Alteromonas, Photobacterium, Pseudoalteromonas and Vibrio in shrimp faeces. these opportunistic pathogenic bacteria constituted up to 60% and 80% of the sequences in samples from the early and advances stages of the disease outbreak, respectively, and exhibited a high degree of co-occurrence. Furthermore, toxR and tlh were detected in water at the disease event only. Notably, bacterial community resilience in water occurred when pH was adjusted to 8. Then WFD ceased without a mortality event. In conclusion, pH was a reliable indicator of the WFD outbreak risk. Dissolved oxygen and compositions of water and intestinal bacteria may also serve as indicators for better prevention of WFD event

Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System

Saharan dust input and seasonal upwelling along North-West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; >3.0 μm) and free-living (FL; 0.2-3.0 μm) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.Fil: Bachmann, Jennifer. Universitat Bremen; Alemania. Leibniz Centre for Tropical Marine Research; AlemaniaFil: Heimbach, Tabea. Leibniz Centre for Tropical Marine Research; Alemania. Universitat Bremen; Alemania. Max Plank Institute for Marine Microbiology; AlemaniaFil: Hassenrück, Christiane. Leibniz Centre for Tropical Marine Research; AlemaniaFil: Kopprio, Germán Adolfo. Leibniz Centre for Tropical Marine Research; Alemania. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; ArgentinaFil: Iversen, Morten Hvitfeldt. Universitat Bremen; Alemania. Alfred Wegener Institute for Polar and Marine Research; AlemaniaFil: Grossart, Hans Peter. Leibniz-Institute of Freshwater Ecology and Inland Fisheries; Alemania. University of Potsdam; AlemaniaFil: Gärdes, Astrid. Leibniz Centre for Tropical Marine Research; Alemani

Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism

Revista Open Access. Artículo con licencia Creative Commons Attribution. -- 11 páginas, 4 figuras, 4 tablas.Marinobacter adhaerens HP15 is the type strain of a newly identified marine species, which is phylogenetically related to M. flavimaris, M. algicola, and M. aquaeolei. It is of special interest for research on marine aggregate formation because it showed specific attachment to diatom cells. In vitro it led to exopolymer formation and aggregation of these algal cells to form marine snow particles. M. adhaerens HP15 is a free-living, motile, rod-shaped, Gram-negative Gammaproteobacterium, which was originally isolated from marine particles sampled in the German Wadden Sea. M. adhaerens HP15 grows heterotrophically on various media, is easy to access genetically, and serves as a model organism to investigate the cellular and molecular interactions with the diatom Thalassiosira weissflogii. Here we describe the complete and annotated genome sequence of M. adhaerens HP15 as well as some details on flagella-associated genes. M. adhaerens HP15 possesses three replicons; the chromosome comprises 4,422,725 bp and codes for 4,180 protein-coding genes, 51 tRNAs and three rRNA operons, while the two circular plasmids are ~187 kb and ~42 kb in size and contain 178 and 52 protein-coding genes, respectively.Peer reviewe

Vibrio and Bacterial Communities Across a Pollution Gradient in the Bay of Bengal: Unraveling Their Biogeochemical Drivers

The highly populated coasts of the Bay of Bengal are particularly vulnerable to water-borne diseases, pollution and climatic extremes. The environmental factors behind bacterial community composition and Vibrio distribution were investigated in an estuarine system of a cholera-endemic region in the coastline of Bangladesh. Higher temperatures and sewage pollution were important drivers of the abundance of toxigenic Vibrio cholerae. A closer relation between non-culturable Vibrio and particulate organic matter (POM) was inferred during the post-monsoon. The distribution of operational taxonomic units (OTUs) of Vibrio genus was likely driven by salinity and temperature. The resuspension of sediments increased Vibrio abundance and organic nutrient concentrations. The δ13C dynamic in POM followed an increasing gradient from freshwater to marine stations; nevertheless, it was not a marker of sewage pollution. Bacteroidales and culturable coliforms were reliable indicators of untreated wastewater during pre and post-monsoon seasons. The presumptive incorporation of depleted-ammonium derived from ammonification processes under the hypoxic conditions, by some microorganisms such as Cloacibacterium and particularly by Arcobacter nearby the sewage discharge, contributed to the drastic 15N depletion in the POM. The likely capacity of extracellular polymeric substances production of these taxa may facilitate the colonization of POM from anthropogenic origin and may signify important properties for wastewater bioremediation. Genera of potential pathogens other than Vibrio associated with sewage pollution were Acinetobacter, Aeromonas, Arcobacter, and Bergeyella. The changing environmental conditions of the estuary favored the abundance of early colonizers and the island biogeography theory explained the distribution of some bacterial groups. This multidisciplinary study evidenced clearly the eutrophic conditions of the Karnaphuli estuary and assessed comprehensively its current bacterial baseline and potential risks. The prevailing conditions together with human overpopulation and frequent natural disasters, transform the region in one of the most vulnerable to climate change. Adaptive management strategies are urgently needed to enhance ecosystem health.Fil: Kopprio, Germán Adolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentina. Leibniz - Institute of Freshwater Ecology and Inland Fisheries; Alemania. Leibniz Center For Tropical Marine Research ; AlemaniaFil: Neogi, Sucharit Basu. Osaka Prefecture University; JapónFil: Rashid, Harunur. Bangladesh Agricultural University; BangladeshFil: Alonso, Cecilia. Universidad de la República. Centro Universitario Regional del Este; UruguayFil: Yamasaki, Shinji. Osaka Prefecture University; JapónFil: Koch, Boris Peter. Alfred-Wegener-Institut. Helmholtz-Zentrum für Polar und Meeresforschung; AlemaniaFil: Gärdes, Astrid. Leibniz Center For Tropical Marine Research; AlemaniaFil: Lara, Ruben Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentin

Carrageenophyte-attached and planktonic bacterial communities in two distinct bays of Vietnam: Eutrophication indicators and insights on ice-ice disease

The composition of the bacterial community of carrageenophyte-attached and planktonic bacteria was studied in two bays of Vietnam with contrasting anthropogenic inputs to assess their role as ecological indicators. Clear differences (~73% dissimilarity) between carrageenophyte-attached bacteria and bacterioplankton were detected in terms of genus composition: mainly Agaribacter, Ruegeria, Alteromonas, the Pir4 lineage and Vibrio for the carrageenophytes and Candidatus Actinomarina, HIMB 11, NS groups and SAR clades for the bacterioplankton. The copiotrophic nature, potential for complex-polymer degradation, and ability to form and defend biofilms were common features inferred for the carrageenophyte-attached microbiome. Significant differences between the bays were detected in the concentration of most inorganic nutrients. More eutrophic conditions and presumptive wastewater pollution in Cam Ranh (CR) bay were primarily indicated by the dominance of Rubripirellula, Leptobacterium, Hypnocyclicus and Porphyrobacter and their correlations with phosphate. In terms of bacterioplankton, the influence of intensive aquaculture in CR bay was suggested by the dominance of the NS5 and NS4 marine groups, the SUP05 cluster, Flavobacteriaceae unclassified and SAR 11 clade III as well as their strong correlations with ammonium and phosphate. The link between silicate and other inorganic nutrients suggests freshwater input in CR bay. Arenicellaceae unclassified and Formosa were also potential indicators of eutrophication. Operational taxonomic units (OTUs) of Marinagarivorans, Cobetia, Vibrio, Alteromonas and Pseudoalteromonas were typical of the carrageenophytes showing ice-ice disease symptoms. Vibrio and Alteromonas were also common among healthy macroalgae, and differences at the OTU level suggested potential succession of species from the healthy to the diseased state. The probable beneficial roles of some bacteria, such as Ruegeria, Cutibacterium and unidentified members of the family Rhizobiaceae, were discussed. This study provides pioneering insights into the bacterial community composition of carrageenophytes and highlights their ecological value as strong indicators of the sources of organic matter, anthropogenic impacts and health status of marine systems.Fil: Kopprio, Germán Adolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentina. Leibniz - Institute of Freshwater Ecology and Inland Fisheries; Alemania. Vietnam Academy of Science and Technology. Institute of Natural Product Chemistry; VietnamFil: Cuong, Le Huu. Vietnam Academy of Science and Technology. Graduate University of Science and Technology; Vietnam. Vietnam Academy of Science and Technology. Institute of Natural Product Chemistry; VietnamFil: Luyen, Nguyen Dinh. Vietnam Academy of Science and Technology. Graduate University of Science and Technology; Vietnam. Vietnam Academy of Science and Technology. Institute of Natural Product Chemistry; VietnamFil: Duc, Tran Mai. Vietnam Academy of Science and Technology. Nhatrang Institute of Technology Research and Application; VietnamFil: Ha, Tran Hong. Vietnam Academy of Science and Technology. Graduate University of Science and Technology; VietnamFil: Huong, Le Mai. Vietnam Academy of Science and Technology. Institute of Natural Product Chemistry; Vietnam. Vietnam Academy of Science and Technology. Graduate University of Science and Technology; VietnamFil: Gärdes, Astrid. Leibniz - Institute of Freshwater Ecology and Inland Fisheries; Alemania. University of Applied Sciences; Alemania. Alfred-Wegener-Institut. Helmholtz-Zentrum für Polar und Meeresforschung; Alemani

Spatio-temporal patterns in the coral reef communities of the Spermonde Archipelago, 2012–2014, II: Fish assemblages display structured variation related to benthic condition

The Spermonde Archipelago is a complex of ~70 mostly populated islands off Southwest Sulawesi, Indonesia, in the center of the Coral Triangle. The reefs in this area are exposed to a high level of anthropogenic disturbances. Previous studies have shown that variation in the benthos is strongly linked to water quality and distance from the mainland. However, little is known about the fish assemblages of the region and if their community structure also follows a relationship with benthic structure and distance from shore. In this study, we used eight islands of the archipelago, varying in distance from 1 to 55 km relative to the mainland, and 3 years of surveys, to describe benthic and fish assemblages and to examine the spatial and temporal influence of benthic composition on the structure of the fish assemblages. Cluster analysis indicated that distinct groups of fish were associated with distance, while few species were present across the entire range of sites. Relating fish communities to benthic composition using a multivariate generalized linear model confirmed that fish groups relate to structural complexity (rugosity) or differing benthic groups; either algae, reef builders (coral and crustose coralline algae) or invertebrates and rubble. From these relationships we can identify sets of fish species that may be lost given continued degradation of the Spermonde reefs. Lastly, the incorporation of water quality, benthic and fish indices indicates that local coral reefs responded positively after an acute disturbance in 2013 with increases in reef builders and fish diversity over relatively short (1 year) time frames. This study contributes an important, missing component (fish community structure) to the growing literature on the Spermonde Archipelago, a system that features environmental pressures common in the greater Southeast Asian region

Spatio-temporal patterns in coral reef communities of the Spermonde Archipelago, 2012-2014, I: Comprehensive reef monitoring of water and benthic indicators reflect changes in reef health

Pollution, fishing, and outbreaks of predators can heavily impact coastal coral reef ecosystems, leading to decreased water quality and benthic community shifts. To determine the main environmental drivers of coral reef status in the Spermonde Archipelago, Indonesia, we monitored environmental variables and coral reef benthic community structure along an on-to-offshore gradient annually from 2012 to 2014. Findings revealed that concentrations of phosphate, chlorophyll a-like fluorescence, suspended particulate matter, and light attenuation significantly decreased from on-to-offshore, while concentrations of dissolved O2 and values of water pH significantly increased on-to-offshore. Nitrogen stable isotope signatures of sediment and an exemplary common brown alga were significantly enriched nearshore, identifying wastewater input from the city of Makassar as primary N source. In contrast to the high temporal variability in water quality, coral reef benthic community cover did not show strong temporal, but rather, spatial patterns. Turf algae was the dominant group next to live coral, and was negatively correlated to live coral, crustose coralline algae (CCA), rubble and hard substrate. Variation in benthic cover along the gradient was explained by water quality variables linked to trophic status and physico-chemical variables. As an integrated measure of reef status and structural complexity, the benthic index, based on the ratio of relative cover of live coral and CCA to other coral reef organisms, and reef rugosity were determined. The benthic index was consistently low nearshore and increased offshore, with high variability in the midshelf sites across years. Reef rugosity was also lowest nearshore and increased further offshore. Both indices dropped in 2013, increasing again in 2014, indicating a period of acute disturbance and recovery within the study and suggesting that the mid-shelf reefs are more resilient to disturbance than nearshore reefs. We thus recommend using these two indices with a selected number of environmental variables as an integral part of future reef monitoring

Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System

Saharan dust input and seasonal upwelling along North–West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; >3.0 μm) and free-living (FL; 0.2–3.0 μm) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions