Dataset Information

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

ABSTRACT: Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

SUBMITTER: Dupont CL

PROVIDER: S-EPMC3937345 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

Dupont Chris L CL Larsson John J Yooseph Shibu S Ininbergs Karolina K Goll Johannes J Asplund-Samuelsson Johannes J McCrow John P JP Celepli Narin N Allen Lisa Zeigler LZ Ekman Martin M Lucas Andrew J AJ Hagström Åke Å Thiagarajan Mathangi M Brindefalk Björn B Richter Alexander R AR Andersson Anders F AF Tenney Aaron A Lundin Daniel D Tovchigrechko Andrey A Nylander Johan A A JA Brami Daniel D Badger Jonathan H JH Allen Andrew E AE Rusch Douglas B DB Hoffman Jeff J Norrby Erling E Friedman Robert R Pinhassi Jarone J Venter J Craig JC Bergman Birgitta B

PloS one 20140227 2

Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of mic ...[more]

PMID: 24586863

Similar Datasets

Project description:In the recent years anaerobic sludge granulation at elevated salinities in upflow anaerobic sludge blanket (UASB) reactors has been investigated in few engineering based studies, never addressing the microbial community structural role in driving aggregation and keeping granules stability. In this study, the combination of different techniques was applied in order to follow the microbial community members and their structural dynamics in granules formed at low (5 g/L Na+) and high (20 g/L Na+) salinity conditions. Experiments were carried out in four UASB reactors fed with synthetic wastewater, using two experimental set-ups. By applying 16S rRNA gene analysis, the comparison of granules grown at low and high salinity showed that acetotrophic Methanosaeta harundinacea was the dominant methanogen at both salinities, while the dominant bacteria changed. At 5 g/L Na+, cocci chains of Streptoccoccus were developing, while at 20 g/L Na+ members of the family Defluviitaleaceae formed long filaments. By means of Fluorescence in Situ Hybridization (FISH) and Scanning Electron Microscopy (SEM), it was shown that aggregation of Methanosaeta in compact clusters and the formation of filaments of Streptoccoccus and Defluviitaleaceae during the digestion time were the main drivers for the granulation at low and high salinity. Interestingly, when the complex protein substrate (tryptone) in the synthetic wastewater was substituted with single amino acids (proline, leucine and glutamic acid), granules at high salinity (20 g/L Na+) were not formed. This corresponded to a decrease of Methanosaeta relative abundance and a lack of compact clustering, together with disappearance of Defluviitaleaceae and consequent absence of bacterial filaments within the dispersed biomass. In these conditions, a biofilm was growing on the glass wall of the reactor instead, highlighting that a complex protein substrate such as tryptone can contribute to granules formation at elevated salinity.

Project description:The relatively rare freshwater ecosystems in the arid southwestern United States serve as biodiversity hotspots, yet they remain among the most threatened systems in the world due to human impacts and climate change. Globally, arid region wetlands remain understudied with respect to their ecology, making assessments of quality or restoration efforts challenging. To address these needs, this project aims to better understand the factors that drive water quality and macroinvertebrate community composition of wetlands of the US desert Southwest. Water quality and macroinvertebrate data were collected over three years from 14 different wetland and riparian sites spanning across West Texas, New Mexico and Arizona. Principal Component Analysis (PCA) indicated that salinity related variables such as chloride, sulfate and conductivity were the greatest drivers of environmental variance (32%) among sampled desert wetlands. Nutrients such as nitrate and phosphate described a second axis, with 22% of variation in environmental data explained, where we found a clear distinction between wastewater and non-wastewater wetlands. Nutrients were shown to have the greatest impact on macroinvertebrate communities with wetlands receiving wastewater showing more uneven distribution of functional feeding groups and lower Simpson Index scores. These sites were dominated by filter feeders and had lower relative abundances of predator and collector-gatherer taxa. There was also a significant decrease in metrics related to diversity and environmental sensitivity such as % Ephemeroptera-Odonata-Trichoptera (EOT) within high nutrient sites. Increased salinity levels were also shown to correlate with lower Simpson Index scores indicating that increased salinity resulted in a decline in macroinvertebrate diversity and evenness. Overall, the nutrients within effluent water have shown to significantly alter community composition especially in desert wetlands where macroinvertebrates may be more adapted to high salinity. Though macroinvertebrate communities in wastewater sites may not fully resemble those of natural wetlands over time, creation of these sites can still benefit landscape level diversity.Supplementary informationThe online version contains supplementary material available at 10.1007/s13157-022-01647-2.

Project description:BackgroundBacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge.ResultsFour independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These protozoa had a strong, positive-correlation with the initial formation of compact aggregates prior to granule development. Furthermore, chemical inhibition of these ciliates in the floccular sludge delayed the initiation of granule formation. Analysis of the bacterial communities in the thiram treated sludge demonstrated that the recovery of 'Candidatus Accumulibacter' was positively correlated with the formation of compact aggregates and granules.ConclusionPredation by bacteriophage and protozoa were positively correlated with the formation of aerobic granules. Increases in Inoviridae abundance suggested that filamentous phages may promote the structural formation of granules. Initiation of granules formation was delayed due to an absence of protozoa after chemical treatment. The presence of 'Candidatus Accumulibacter' was necessary for the formation of granules in the absence of protozoa.

Dataset Information

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

Publications

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets