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1. Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea)

   https://doi.org/10.1186/s42523-021-00136-x  

   Mika, Katelyn ; Okamoto, Alexander S. ; Shubin, Neil H. ; Mark Welch, David B. ( October 2021 , Animal Microbiome)

   Microbial transmission from parent to offspring is hypothesized to be widespread in vertebrates. However, evidence for this is limited as many evolutionarily important clades remain unexamined. There is currently no data on the microbiota associated with any Chondrichthyan species during embryonic development, despite the global distribution, ecological importance, and phylogenetic position of this clade. In this study, we take the first steps towards filling this gap by investigating the microbiota associated with embryonic development in the little skate,Leucoraja erinacea,a common North Atlantic species and popular system for chondrichthyan biology.

   To assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate,at six points during ontogeny. Community composition was analyzed using the QIIME2 pipeline and microbial continuity between stages was tracked using FEAST.

   We identify site-specific and stage-specific microbiota dominated by the bacterial phylaProteobacteriaandBacteroidetes. This composition is similar to, but distinct from, that of previously published data on the adult microbiota of other chondrichthyan species. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community–particularly on the internal surface of the capsule–and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop.

   Our study is the first exploration of the chondrichthyan microbiota throughout ontogeny and provides the first evidence of vertical transmission in this group.

    

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2. The effect of distal‐end trimming on Saccharina latissima morphology, composition, and productivity

   https://doi.org/10.1111/jwas.12814  

   Grebe, Gretchen S. ; Byron, Carrie J. ; Brady, Damian C. ; St. Gelais, Adam T. ; Costa‐Pierce, Barry A. ( June 2021 , Journal of the World Aquaculture Society)

   As kelp cultivation increases around the world, so does the need for farm management strategies that produce specific crop characteristics, optimize yield, widen harvesting windows, and prevent biomass loss. Distal‐end trimming of macroalgae has been recommended as a farm management method addressing these needs. In this study, we trimmed cultivatedSaccharina latissimasporophytes grown in the Western Gulf of Maine (WGoM) to 60 cm above the stipe–blade interface. We characterized the effect of trimming on the morphology, tissue nutrient content, stable isotope ratio, and nitrate reductase activity of the kelp. We also evaluated the economic trade‐offs of trimming using a simple production model. The results suggest that trimming the blade to 60 cm may have minimal biological consequences. Additionally, the trimming appears to benefit “short” kelp blades in proximity to the trimmed blades. Daily yield (% increase in weight day⁻¹) after trimming was initially lower than the control, but late‐season daily yields and crop‐retention following storms were markedly improved. Ultimately, we conclude that growers could use trimming to acquire kelp biomass earlier in the season, retain late‐season biomass, and potentially increase the total revenue gained from kelp farming if price premiums can be exacted for this biomass.

    

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3. Estuarine gradients dictate spatiotemporal variations of microbiome networks in the Chesapeake Bay

   https://doi.org/10.1186/s40793-021-00392-z  

   Wang, Hualong ; Chen, Feng ; Zhang, Chuanlun ; Wang, Min ; Kan, Jinjun ( November 2021 , Environmental Microbiome)

   Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially in those with long residence time such as the Chesapeake Bay (CB). However, it is unclear how microbial taxa cooccurr and how the inter-taxa networks respond to the strong environmental gradients in the estuaries.

   Here, we constructed co-occurrence networks on prokaryotic microbial communities in the CB, which included seasonal samples from seven spatial stations along the salinity gradients for three consecutive years. Our results showed that spatiotemporal variations of planktonic microbiomes promoted differentiations of the characteristics and stability of prokaryotic microbial networks in the CB estuary. Prokaryotic microbial networks exhibited a clear seasonal pattern where microbes were more closely connected during warm season compared to the associations during cold season. In addition, microbial networks were more stable in the lower Bay (ocean side) than those in the upper Bay (freshwater side). Multivariate regression tree (MRT) analysis and piecewise structural equation modeling (SEM) indicated that temperature, salinity and total suspended substances along with nutrient availability, particulate carbon and Chla, affected the distribution and co-occurrence of microbial groups, such as Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia. Interestingly, compared to the abundant groups (such as SAR11, Saprospiraceae and Actinomarinaceae), the rare taxa including OM60 (NOR5) clade (Gammaproteobacteria), Micrococcales (Actinobacteria), and NS11-12 marine group (Bacteroidetes) contributed greatly to the stability of microbial co-occurrence in the Bay. Modularity and cluster structures of microbial networks varied spatiotemporally, which provided valuable insights into the ‘small world’ (a group of more interconnected species), network stability, and habitat partitioning/preferences.

   Our results shed light on how estuarine gradients alter the spatiotemporal variations of prokaryotic microbial networks in the estuarine ecosystem, as well as their adaptability to environmental disturbances and co-occurrence network complexity and stability.

    

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4. Spatial structure in the “Plastisphere”: Molecular resources for imaging microscopic communities on plastic marine debris

   https://doi.org/10.1111/1755-0998.13119  

   Schlundt, Cathleen ; Mark Welch, Jessica L. ; Knochel, Anna M. ; Zettler, Erik R. ; Amaral‐Zettler, Linda A. ( November 2019 , Molecular Ecology Resources)

   Plastic marine debris (PMD) affects spatial scales of life from microbes to whales. However, understanding interactions between plastic and microbes in the “Plastisphere”—the thin layer of life on the surface of PMD—has been technology‐limited. Research into microbe–microbe and microbe–substrate interactions requires knowledge of community phylogenetic composition but also tools to visualize spatial distributions of intact microbial biofilm communities. We developed a CLASI‐FISH (combinatorial labelling and spectral imaging – fluorescencein situhybridization) method using confocal microscopy to study Plastisphere communities. We created a probe set consisting of three existing phylogenetic probes (targeting all Bacteria,Alpha‐, andGammaproteobacteria) and four newly designed probes (targetingBacteroidetes,Vibrionaceae,RhodobacteraceaeandAlteromonadaceae) labelled with a total of seven fluorophores and validated this probe set using pure cultures. Our nested probe set strategy increases confidence in taxonomic identification because targets are confirmed with two or more probes, reducing false positives. We simultaneously identified and visualized these taxa and their spatial distribution within the microbial biofilms on polyethylene samples in colonization time series experiments in coastal environments from three different biogeographical regions. Comparing the relative abundance of 16S rRNA gene amplicon sequencing data with cell‐count abundance data retrieved from the microscope images of the same samples showed a good agreement in bacterial composition. Microbial communities were heterogeneous, with direct spatial relationships between bacteria, cyanobacteria and eukaryotes such as diatoms but also micro‐metazoa. Our research provides a valuable resource to investigate biofilm development, succession and associations between specific microscopic taxa at micrometre scales.

    

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5. Social environment and genetics underlie body site‐specific microbiomes of Yellowstone National Park gray wolves ( Canis lupus )

   https://doi.org/10.1002/ece3.7767  

   DeCandia, Alexandra L. ; Cassidy, Kira A. ; Stahler, Daniel R. ; Stahler, Erin A. ; vonHoldt, Bridgett M. ( June 2021 , Ecology and Evolution)

   The host‐associated microbiome is an important player in the ecology and evolution of species. Despite growing interest in the medical, veterinary, and conservation communities, there remain numerous questions about the primary factors underlying microbiota, particularly in wildlife. We bridged this knowledge gap by leveraging microbial, genetic, and observational data collected in a wild, pedigreed population of gray wolves (Canis lupus) inhabiting Yellowstone National Park. We characterized body site‐specific microbes across six haired and mucosal body sites (and two fecal samples) using 16S rRNA amplicon sequencing. At the phylum level, we found that the microbiome of gray wolves primarily consists of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria, consistent with previous studies within Mammalia and Canidae. At the genus level, we documented body site‐specific microbiota with functions relevant to microenvironment and local physiological processes. We additionally employed observational and RAD sequencing data to examine genetic, demographic, and environmental correlates of skin and gut microbiota. We surveyed individuals across several levels of pedigree relationships, generations, and social groups, and found that social environment (i.e., pack) and genetic relatedness were two primary factors associated with microbial community composition to differing degrees between body sites. We additionally reported body condition and coat color as secondary factors underlying gut and skin microbiomes, respectively. We concluded that gray wolf microbiota resemble similar host species, differ between body sites, and are shaped by numerous endogenous and exogenous factors. These results provide baseline information for this long‐term study population and yield important insights into the evolutionary history, ecology, and conservation of wild wolves and their associated microbes.

    

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