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1. Mill dams impact microbiome structure and depth distribution in riparian sediments

   https://doi.org/10.3389/fmicb.2023.1161043  

   Kan, Jinjun ; Peck, Erin K. ; Zgleszewski, Laura ; Peipoch, Marc ; Inamdar, Shreeram ( June 2023 , Frontiers in Microbiology)

   Introduction Damming has substantially fragmented and altered riverine ecosystems worldwide. Dams slow down streamflows, raise stream and groundwater levels, create anoxic or hypoxic hyporheic and riparian environments and result in deposition of fine sediments above dams. These sediments represent a good opportunity to study human legacies altering soil environments, for which we lack knowledge on microbial structure, depth distribution, and ecological function. Methods Here, we compared high throughput sequencing of bacterial/ archaeal and fungal community structure (diversity and composition) and functional genes (i.e., nitrification and denitrification) at different depths (ranging from 0 to 4 m) in riparian sediments above breached and existing milldams in the Mid-Atlantic United States. Results We found significant location- and depth-dependent changes in microbial community structure. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi, Acidobacteria, Planctomycetes, Thaumarchaeota, and Verrucomicrobia were the major prokaryotic components while Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Mucoromycota, and Rozellomycota dominated fungal sequences retrieved from sediment samples. Ammonia oxidizing genes ( amo A for AOA) were higher at the sediment surface but decreased sharply with depth. Besides top layers, denitrifying genes ( nos Z) were also present at depth, indicating a higher denitrification potential in the deeper layers. However, these results contrasted with in situ denitrification enzyme assay (DEA) measurements, suggesting the presence of dormant microbes and/or other nitrogen processes in deep sediments that compete with denitrification. In addition to enhanced depth stratification, our results also highlighted that dam removal increased species richness, microbial diversity, and nitrification. Discussion Lateral and vertical spatial distributions of soil microbiomes (both prokaryotes and fungi) suggest that not only sediment stratification but also concurrent watershed conditions are important in explaining the depth profiles of microbial communities and functional genes in dammed rivers. The results also provide valuable information and guidance to stakeholders and restoration projects. 

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2. Nitrogen driven niche differentiation in bacterioplankton communities of northeast coastal Bay of Bengal

   https://doi.org/10.1088/2515-7620/ac5a69  

   Ghosh, Anwesha ; Woodward, E Malcolm ; Saha, Ratul ; Nelson, Craig E ; Bhadury, Punyasloke ( March 2022 , Environmental Research Communications)

   Abstract The Bay of Bengal receives nitrogen inputs from multiple sources and the potential role of nitrogen-metabolizing microbial communities in the surface water is not well understood. The nitrogen budget estimate shows a deficit of 4.7 ± 2.4 Tg N yr -1 , suggesting a significant role of dissolved organic nitrogen remineralization in fuelling ecosystem processes. Unravelling the process of remineralization leading to increasing concentrations of dissolved inorganic nitrogen (DIN) in coastal ecosystems such as in mangroves require a better understanding of the composition of functional resident bacterioplankton communities. Bacterioplankton communities were elucidated from eight stations along different estuaries spanning west to east of northeast coastal Bay of Bengal to understand the influence of DIN on shaping these communities. The eight stations were differentiated into ‘low’ and ‘high’ DIN stations based on DIN concentration, with five stations with High DIN concentration (>45 μ M) and three stations with Low DIN concentration (<40 μ M). The V3–V4 region of 16S rRNA was amplified and sequenced to elucidate resident bacterioplankton community structure from environmental DNA. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant bacterioplankton phyla across all stations. Nitrogen-fixing groups such as Nitrospirae, Lentisphaerae, Chloroflexi, and Planctomycetes make up about 1% of the bacterioplankton communities. Abundances of Spirochaetes and Tenericutes showed a positive correlation with DIN. Pseudomonadales, Alteromonadales, and Desulfovibrionales were found to distinctly vary in abundance between Low and High DIN stations. Predicted metagenomic profiles from taxonomically derived community structures indicated bacterial nitrate-nitrite reductase to be negatively correlated with prevalent DIN concentration in High DIN stations but positively correlated in Low DIN stations. This trend was also consistent for genes encoding for nitrate/nitrite response regulators and transporter proteins. This indicates the need to delineate functional bacterioplankton community structures to better understand their role in influencing rates and fluxes of nitrogen within mangroves. 

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3. Trait-Based Comparison of Coral and Sponge Microbiomes

   https://doi.org/10.1038/s41598-020-59320-9  

   Fiore, Cara L. ; Jarett, Jessica K. ; Steinert, Georg ; Lesser, Michael P. ( February 2020 , Scientific Reports)

   Corals and sponges harbor diverse microbial communities that are integral to the functioning of the host. While the taxonomic diversity of their microbiomes has been well-established for corals and sponges, their functional roles are less well-understood. It is unclear if the similarities of symbiosis in an invertebrate host would result in functionally similar microbiomes, or if differences in host phylogeny and environmentally driven microhabitats within each host would shape functionally distinct communities. Here we addressed this question, using metatranscriptomic and 16S rRNA gene profiling techniques to compare the microbiomes of two host organisms from different phyla. Our results indicate functional similarity in carbon, nitrogen, and sulfur assimilation, and aerobic nitrogen cycling. Additionally, there were few statistical differences in pathway coverage or abundance between the two hosts. For example, we observed higher coverage of phosphonate and siderophore metabolic pathways in the star coral,Montastraea cavernosa, while there was higher coverage of chloroalkane metabolism in the giant barrel sponge,Xestospongia muta. Higher abundance of genes associated with carbon fixation pathways was also observed inM. cavernosa, while inX. mutathere was higher abundance of fatty acid metabolic pathways. Metagenomic predictions based on 16S rRNA gene profiling analysis were similar, and there was high correlation between the metatranscriptome and metagenome predictions for both hosts. Our results highlight several metabolic pathways that exhibit functional similarity in these coral and sponge microbiomes despite the taxonomic differences between the two microbiomes, as well as potential specialization of some microbially based metabolism within each host.

    

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4. The gut bacterial microbiome of the Threeridge mussel, Amblema plicata , varies between rivers but shows a consistent core community

   https://doi.org/10.1111/fwb.13905  

   Lawson, Lauren A. ; Atkinson, Carla L. ; Jackson, Colin R. ( March 2022 , Freshwater Biology)

   Freshwater mussels are important for nutrient cycling and ecosystem health as they filter feed on their surrounding water. This filter feeding makes these bivalves especially sensitive to conditions in their environment. Gut microbial communities (microbiomes) have been recognised as important to both host organism and ecosystem health; however, how freshwater mussel microbiomes are organised and influenced is unclear.

   In this study, the gut bacterial microbiome of Threeridge mussel,Amblema plicata, was compared across two river basins, five rivers, and nine local sites in the south‐eastern U.S.A. Mussel gut tissue was dissected, DNA extracted, and the microbiome characterised by high throughput sequencing of the V4 region of the 16S ribosomal RNA gene.

   Planctomycetes, Firmicutes, and Cyanobacteria were the most common bacterial phyla within the guts of all sampledA.plicata. However, the relative abundances of these major bacterial phyla differed between mussels sampled from different rivers and river basins, as did the relative abundance of specific bacterial operational taxonomic units (OTUs). Despite these differences, a core microbiome was identified across all mussels, with eight OTUs being consistent members of theA.plicatamicrobiome at all sites, the most abundant OTU identifying as a member of the family Planctomycetaceae. Geographic distance between sites was not correlated with similarity in the structure of the gut microbiome, which was more related to site physicochemistry.

   Overall, these results suggest that while physicochemical conditions affect the composition of transient bacteria in the Threeridge mussel gut microbiome, the core microbiome is largely unaffected, and a portion of theA.plicatamicrobiome is retained regardless of the river system.

   How long transient bacteria remain in the gut, and to what extent these transient microbes aid in host function is still unknown. Core microbiota have been found to aid in multiple functions within animal hosts, and within freshwater mussels this core microbiome may aid in nutrient processing and cycling. Therefore, it is important to look at both transient and core microbes when studying the structure of freshwater invertebrate microbiomes.

    

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5. Hydrology shapes microbial communities and microbiome‐mediated growth of an Everglades tree island species

   https://doi.org/10.1111/rec.13677  

   Almeida, Brianna K. ; Cline, Eric ; Sklar, Fred ; Afkhami, Michelle E. ( April 2022 , Restoration Ecology)

   Plant‐associated microbiomes can improve plant fitness by ameliorating environmental stress, providing a promising avenue for improving outplantings during restoration. However, the effects of water management on these microbial communities and their cascading effects on primary producers are unresolved for many imperiled ecosystems. One such habitat, Everglades tree islands, has declined by 54% in some areas, releasing excess nutrients into surrounding wetlands and exacerbating nutrient pollution. We conducted a factorial experiment, manipulating the soil microbiome and hydrological regime experienced by a tree island native,Ficus aurea, to determine how microbiomes impact growth under two hydrological management plans. All plants were watered to simulate natural precipitation, but plants in the “unconstrained” management treatment were allowed to accumulate water above the soil surface, while the “constrained” treatment had a reduced stage to avoid soil submersion. We found significant effects of the microbiomes on overall plant performance and aboveground versus belowground investment; however, these effects depended on hydrological treatment. For instance, microbiomes increased investment in roots relative to aboveground tissues, but these effects were 142% stronger in the constrained compared to unconstrained water regime. Changes in hydrology also resulted in changes in the prokaryotic community composition, including a >20 log₂fold increase in the relative abundance of Rhizobiaceae, and hydrology‐shifted microbial composition was linked to changes in plant performance. Our results suggest that differences in hydrological management can have important effects on microbial communities, including taxa often involved in nitrogen cycling, which can in turn impact plant performance.

    

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