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1. Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

   https://doi.org/doi:10.3389/fmicb.2021.616730  

   George, Scott F ; Fierer, Noah ; Levy, Joseph S ; Adams, Byron ( January 2021 , Frontiers in microbiology)

   Zucconi, Laura (Ed.)

   Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteriamore »phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.« less
2. Environmental Drivers of Nearshore Fish Community Composition and Size Structure in Glacially Influenced Gulf of Alaska Estuaries

   https://doi.org/10.1007/s12237-022-01057-x  

   Lundstrom, Nina C. ; Beaudreau, Anne H. ; Mueter, Franz J. ; Konar, Brenda ( February 2022 , Estuaries and Coasts)

   Abstract Coastal ecosystems in Alaska are undergoing rapid change due to warming and glacier recession. We used a natural gradient of glacierized to non-glacierized watersheds (0–60% glacier coverage) in two regions along the Gulf of Alaska—Kachemak Bay and Lynn Canal—to evaluate relationships between local environmental conditions and estuarine fish communities. Multivariate analyses of fish community data collected from five sites per region in 2019 showed that region accounted for the most variation in community composition, suggesting that local effects of watershed type were masked by regional-scale variables. Seasonal shifts in community composition were driven largely by the influx of juvenile Pacific salmon ( Oncorhynchus spp.) in late spring. Spatiotemporal differences among fish communities were partly explained by salinity and temperature, which accounted for 19.5% of the variation in community composition. We used a multi-year dataset from Lynn Canal (2014–2019) to examine patterns of mean length for two dominant species. Generalized additive mixed models indicated that Pacific staghorn sculpin ( Leptocottus armatus ) mean length varied along site-specific seasonal gradients, increasing gradually through the summer in the least glacially influenced sites and increasing rapidly to an asymptote of ~ 150 mm in the most glacially influenced sites. Starry flounder ( Platichthys stellatus ) meanmore »length was more strongly related to environmental conditions, increasing with temperature and turbidity. Together, our findings suggest that community compositions of estuarine fishes show greater variation at the regional scale than the watershed scale, but species-specific variation in size distributions may indicate differences in habitat quality across watershed types within regions.« less
3. Geography and elevation as drivers of cloacal microbiome assemblages of a passerine bird distributed across Sulawesi, Indonesia

   https://doi.org/10.1186/s42523-022-00219-3  

   Joakim, Rachael L. ; Irham, Mohammad ; Haryoko, Tri ; Rowe, Karen M. C. ; Dalimunthe, Yohanna ; Anita, Syahfitri ; Achmadi, Anang S. ; McGuire, Jimmy A. ; Perkins, Susan ; Bowie, Rauri C. K. ( January 2023 , Animal Microbiome)

   Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler,Pellorneum celebense,from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition.

   The five most prevalent bacterial phyla within the gut microbiome ofP. celebensewereProteobacteria(32.6%),Actinobacteria(25.2%),Firmicutes(22.1%),Bacteroidetes(8.7%), andPlantomycetes(2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV ofClostridiumwas enriched in higher elevation samples, while lower elevation samples were enriched with the generaPerlucidibaca(FamilyMoraxellaceae),Lachnoclostridium(FamilyLachnospiraceae), and an unidentified species in the FamilyPseudonocardiaceae.

   While themore »core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance ofClostridiumat high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.

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4. C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data

   https://doi.org/10.1186/s12859-022-05027-9  

   Song, Kuncheng ; Zhou, Yi-Hui ( November 2022 , BMC Bioinformatics)

   Studying the co-occurrence network structure of microbial samples is one of the critical approaches to understanding the perplexing and delicate relationship between the microbe, host, and diseases. It is also critical to develop a tool for investigating co-occurrence networks and differential abundance analyses to reveal the disease-related taxa–taxa relationship. In addition, it is also necessary to tighten the co-occurrence network into smaller modules to increase the ability for functional annotation and interpretability of  these taxa-taxa relationships.  Also, it is critical to retain the phylogenetic relationship among the taxa to identify differential abundance patterns, which can be used to resolve contradicting functions reported by different studies.

   In this article, we present Correlation and Consensus-based Cross-taxonomy Network Analysis (C3NA), a user-friendly R package for investigating compositional microbial sequencing data to identify and compare co-occurrence patterns across different taxonomic levels. C3NA contains two interactive graphic user interfaces (Shiny applications), one of them dedicated to the comparison between two diagnoses, e.g., disease versus control. We used C3NA to analyze two well-studied diseases, colorectal cancer, and Crohn’s disease. We discovered clusters of study and disease-dependent taxa that overlap with known functional taxa studied by other discovery studies and differential abundance analyses.

   C3NA offers amore »new microbial data analyses pipeline for refined and enriched taxa–taxa co-occurrence network analyses, and the usability was further expanded via the built-in Shiny applications for interactive investigation.

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5. Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats

   https://doi.org/10.1093/femsec/fiac040  

   Ferrer, Astrid ; Heath, Katy D. ; Mosquera, Sergio L. ; Suaréz, Yaraví ; Dalling, James W. ( April 2022 , FEMS Microbiology Ecology)

   Wood decomposition in water is a key ecosystem process driven by diverse microbial taxa that likely differ in their affinities for freshwater, estuarine and marine habitats. How these decomposer communities assemble in situ or potentially colonize from other habitats remains poorly understood. At three watersheds on Coiba Island, Panama, we placed replicate sections of branch wood of a single tree species on land, and in freshwater, estuarine and marine habitats that constitute a downstream salinity gradient. We sequenced archaea, bacteria and fungi from wood samples collected after 3, 9 and 15 months to examine microbial community composition, and to examine habitat specificity and abundance patterns. We found that these microbial communities were broadly structured by similar factors, with a strong effect of salinity, but little effect of watershed identity on compositional variation. Moreover, common aquatic taxa were also present in wood incubated on land. Our results suggest that either taxa dispersed to both terrestrial and aquatic habitats, or microbes with broad habitat ranges were initially present in the wood as endophytes. Nonetheless, these habitat generalists varied greatly in abundance across habitats suggesting an important role for habitat filtering in maintaining distinct aquatic communities in freshwater, estuarine and marine habitats.