Fine-scale temporal dynamics of a fragmented lotic microbial ecosystem

Quantifying the Importance of Abiotic and Biotic Factors Governing the Succession of Gut Microbiota Over Shrimp Ontogeny

Intensive studies have evaluated abiotic factors in shaping host gut microbiota. In contrast, little is known on how and to what extent abiotic (geochemical variables) and biotic (i.e., surrounding microbes, younger shrimp, and age) factors assemble the gut microbiota over shrimp ontogeny. Considering the functional importance of gut microbiota in improving host fitness, this knowledge is fundamental to sustain a desirable gut microbiota for a healthy aquaculture. Here, we characterized the successional rules of both the shrimp gut and rearing water bacterial communities over the entire shrimp farming. Both the gut and rearing water bacterial communities exhibited the time decay of similarity relationship, with significantly lower temporal turnover rate for the gut microbiota, which were primarily governed by shrimp age (days postlarval inoculation) and water pH. Gut commensals were primary sourced (averaged 60.3%) from their younger host, rather than surrounding bacterioplankton (19.1%). A structural equation model revealed that water salinity, pH, total phosphorus, and dissolve oxygen directly governed bacterioplankton communities but not for the gut microbiota. In addition, shrimp gut microbiota did not simply mirror the rearing bacterioplankton communities. The gut microbiota tended to be governed by variable selection over shrimp ontogeny, while the rearing bacterioplankton community was shaped by homogeneous selection. However, the determinism of rare and stochasticity of abundant subcommunities were consistent between shrimp gut and rearing water. These findings highlight the importance of independently interpreting host-associated and free-living communities, as well as their rare and abundant subcommunities for a comprehensive understanding of the ecological processes that govern microbial successions.

Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation

Bioremediation, based on the use of microorganisms to break down pollutants, can be very effective at reducing soil pollution. But the climate change we are now experiencing is bound to have an impact on bioremediation performance, since the activity and degrading abilities of soil microorganisms are dependent on a series of environmental parameters that are themselves being altered by climate change, such as soil temperature, moisture, amount of root exudates, etc. Many climate-induced effects on soil microorganisms occur indirectly through changes in plant growth and physiology derived from increased atmospheric CO2 concentrations and temperatures, the alteration of precipitation patterns, etc., with a concomitant effect on rhizoremediation performance (i.e. the plant-assisted microbial degradation of pollutants in the rhizosphere). But these effects are extremely complex and mediated by processes such as acclimation and adaptation. Besides, soil microorganisms form complex networks of interactions with a myriad of organisms from many taxonomic groups that will also be affected by climate change, further complicating data interpretation.

Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

Urbanization strongly influences headwater stream chemistry and hydrology, but little is known about how these conditions impact bacterial community composition. We predicted that urbanization would impact bacterial community composition, but that stream water column bacterial communities would be most strongly linked to urbanization at a watershed-scale, as measured by impervious cover, while sediment bacterial communities would correlate with environmental conditions at the scale of stream reaches. To test this hypothesis, we determined bacterial community composition in the water column and sediment of headwater streams located across a gradient of watershed impervious cover using high-throughput 16S rRNA gene amplicon sequencing. Alpha diversity metrics did not show a strong response to catchment urbanization, but beta diversity was significantly related to watershed impervious cover with significant differences also found between water column and sediment samples. Samples grouped primarily according to habitat—water column vs. sediment—with a significant response to watershed impervious cover nested within each habitat type. Compositional shifts for communities in urbanized streams indicated an increase in taxa associated with human activity including bacteria from the genus Polynucleobacter, which is widespread, but has been associated with eutrophic conditions in larger water bodies. Another indicator of communities in urbanized streams was an OTU from the genus Gallionella, which is linked to corrosion of water distribution systems. To identify changes in bacterial community interactions, bacterial co-occurrence networks were generated from urban and forested samples. The urbanized co-occurrence network was much smaller and had fewer co-occurrence events per taxon than forested equivalents, indicating a loss of keystone taxa with urbanization. Our results suggest that urbanization has significant impacts on the community composition of headwater streams, and suggest that processes driving these changes in urbanized water column vs. sediment environments are distinct.

The temporal scaling of bacterioplankton composition: high turnover and predictability during shrimp cultivation

The spatial distribution of microbial communities has recently been reliably documented in the form of a distance-similarity decay relationship. In contrast, temporal scaling, the pattern defined by the microbial similarity-time relationships (STRs), has received far less attention. As a result, it is unclear whether the spatial and temporal variations of microbial communities share a similar power law. In this study, we applied the 454 pyrosequencing technique to investigate temporal scaling in patterns of bacterioplankton community dynamics during the process of shrimp culture. Our results showed that the similarities decreased significantly (P = 0.002) with time during the period over which the bacterioplankton community was monitored, with a scaling exponent of w = 0.400. However, the diversities did not change dramatically. The community dynamics followed a gradual process of succession relative to the parent communities, with greater similarities between samples from consecutive sampling points. In particular, the variations of the bacterial communities from different ponds shared similar successional trajectories, suggesting that bacterial temporal dynamics are predictable to a certain extent. Changes in bacterial community structure were significantly correlated with the combination of Chl a, TN, PO4 (3-), and the C/N ratio. In this study, we identified predictable patterns in the temporal dynamics of bacterioplankton community structure, demonstrating that the STR of the bacterial community mirrors the spatial distance-similarity decay model.

Investigating a lotic microbial community following a severe detergent spill

A large non-ionic detergent spill affected the Yarqon stream, where water sampling was performed prior to the spill as a part of the stream's routine sampling and during and after the event. Following the spill, a large foam layer was observed for about 3-4 days accompanied by death of all fauna in the stream. Despite a large quantity of freshwater that was introduced to the stream as an emergency measure, a drastic decrease in dissolved oxygen was also observed. A rapid reduction in bacterial diversity and richness, as measured by automated ribosomal intergenic spacer analysis, was also evident, as microbial assemblages changes accompanied pollutant exposure. However, this analysis showed that the microbial assemblages of the stream were quick to recover and became similar to pre-spill communities as early as a week after the spill. These findings suggest that bacterial assemblages are much more robust to large anthropogenic disturbances than expected.

In situ transplant analysis of free-living bacteria in a lotic ecosystem

The Yarqon is a slow-flowing Mediterranean stream with three ecologically distinct sections, with varying abiotic conditions and anthropogenic influences. We used the Yarqon as a test habitat to study the effect of flow on microbial communities. Stream water samples from three distinct abiotic conditions: "clean", "human-impacted" and "brackish" sections were incubated in situ in dialysis bags at each of these sections for approximately 73 h. The samples were retrieved and analyzed by ARISA (automated ribosomal internal spacer analysis) and viable counts. Diversity estimates showed that free-living assemblages from the middle human-impacted section increased in diversity, while assemblages from the upper-clean section decreased in diversity unless planted in their site of origin. Samples originating from the brackish western section decreased in diversity wherever they were incubated. The ARISA profiles of the samples usually grouped by origin rather than by incubation location, implying that the rate of change of the free-living bacterial assemblages due to the shift in environment is relatively slow. Nevertheless, introducing free-living bacteria from the human-impacted section into the freshwater section resulted in a profile more similar to the latter, indicating a profound niche influence on these microbial assemblages.