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1. Environmental controls on pteropod biogeography along the Western Antarctic Peninsula

   https://doi.org/10.1002/lno.11041  

   Thibodeau, P. S. ; Steinberg, D. K. ; Stammerjohn, S. E. ; Hauri, C. ( October 2018 , Limnology and Oceanography)

   Pteropods are abundant zooplankton in the Western Antarctic Peninsula (WAP) and important grazers of phytoplankton and prey for higher trophic levels. We analyzed long‐term (1993–2017) trends in summer (January–February) abundance of WAP pteropods in relation to environmental controls (sea ice, sea surface temperature, climate indices, phytoplankton biomass and productivity, and carbonate chemistry) and interspecies dynamics using general linear models. There was no overall directional trend in abundance of thecosomes,Limacina helicina antarcticaandClio pyramidata,throughout the entire WAP, althoughL. antarcticaabundance increased in the slope region andC. pyramidataabundance increased in the South. HighL. antarcticaabundance was strongly tied to a negative Multivariate El Niño Southern Oscillation Index the previous year.C. pyramidataabundance was best explained by early sea ice retreat 1‐yr prior. Abundance of the gymnosome species,Clione antarcticaandSpongiobranchaea australis, increased over the time series, particularly in the slope region. Gymnosome abundance was positively influenced by abundance of their prey,L. antarctica,during the same season, and late sea ice advance 2‐yr prior. These trends indicate a shorter ice season promotes longer periods of open water in spring/summer favoring all pteropod species. Weak relationships were found between pteropod abundance and carbonate chemistry, and no long‐term trend in carbonate parameters was detected. These factors indicate ocean acidification is not presently influencing WAP pteropod abundance. Pteropods are responsive to the considerable environmental variability on both temporal and spatial scales—key for predicting future effects of climate change on regional carbon cycling and plankton trophic interactions.

    

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2. Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies

   https://doi.org/10.1093/icb/icac045  

   Kohl, Kevin D. ; Dieppa-Colón, Etan ; Goyco-Blas, José ; Peralta-Martínez, Karen ; Scafidi, Luke ; Shah, Sarth ; Zawacki, Emma ; Barts, Nick ; Ahn, Young ; Hedayati, Stefanie ; et al ( May 2022 , Integrative And Comparative Biology)

   The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus); and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genus Ruminococcus and highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarily Bacillus and Enterococcus), with some capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology.

    

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3. Extensive variability in the gut microbiome of a highly‐specialized and critically endangered lemur species across sites

   https://doi.org/10.1002/ajp.23046  

   Donohue, Mariah E. ; Asangba, Abigail E. ; Ralainirina, Jocelyn ; Weisrock, David W. ; Stumpf, Rebecca M. ; Wright, Patricia C. ( September 2019 , American Journal of Primatology)

   Deforestation continues to jeopardize Malagasy primates as viable habitats become smaller, more fragmented, and more disturbed. This deforestation can lead to changes in diet, microhabitat, and gene flow between populations of endangered species, and it remains unclear how these changes may affect gut microbiome (GM) characteristics. The black‐and‐white ruffed lemur (Varecia variegata), which is among Madagascar's most threatened lemur species, provides a critical model for understanding the relationships between historical and on‐going deforestation (habitat disturbance), feeding ecology, and GM composition and diversity. We studied four populations inhabiting two rainforests (relatively pristine vs. highly disturbed) in southeastern Madagascar. We conducted full‐day focal animal behavioral follows and collected fecal samples opportunistically across a three‐month period. Our results indicate that lemurs inhabiting sites characterized by habitat disturbance and low dietary diversity exhibited reduced gut microbial alpha diversity. We also show that these same factors were associated with high community dissimilarity using weighted and unweighted UniFrac metrics. Finally, an indicator species analysis showed that the most pristine site was characterized by an abundance of methanogenic archaea. While it is impossible to disentangle the relative contributions of each confounding variable presented by our sampling design, these results provide crucial information about GM variability, thereby underscoring the importance of monitoring endangered species at the population‐level.

    

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4. Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis

   https://doi.org/10.1038/s43705-023-00323-8  

   Gutiérrez-García, Karina ; Whitaker, Melissa R. L. ; Bustos-Díaz, Edder D. ; Salzman, Shayla ; Ramos-Aboites, Hilda E. ; Reitz, Zachary L. ; Pierce, Naomi E. ; Cibrián-Jaramillo, Angélica ; Barona-Gómez, Francisco ( November 2023 , ISME Communications)

   Ingestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich cycads with apparent immunity. Some cycad-feeding insects possess a common set of gut bacteria, which might play a role in detoxifying cycad toxins. Here, we investigated the composition of gut microbiota from a worldwide sample of cycadivorous insects and characterized the biosynthetic potential of selected bacteria. Cycadivorous insects shared a core gut microbiome consisting of six bacterial taxa, mainly belonging to the Proteobacteria, which we were able to isolate. To further investigate selected taxa from diverging lineages, we performed shotgun metagenomic sequencing of co-cultured bacterial sub-communities. We characterized the biosynthetic potential of four bacteria from Serratia, Pantoea, and two different Stenotrophomonas lineages, and discovered a suite of biosynthetic gene clusters notably rich in siderophores. Siderophore semi-untargeted metabolomics revealed a broad range of chemically related yet diverse iron-chelating metabolites, including desferrioxamine B, suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway that remains to be identified. These results provide a foundation for future investigations into how cycadivorous insects tolerate diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores.

    

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5. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

   https://doi.org/10.1186/s40168-021-01213-8  

   Zhou, Zhichao ; Tran, Patricia Q. ; Breister, Adam M. ; Liu, Yang ; Kieft, Kristopher ; Cowley, Elise S. ; Karaoz, Ulas ; Anantharaman, Karthik ( February 2022 , Microbiome)

   Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling.

   We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut.

   METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 athttps://github.com/AnantharamanLab/METABOLIC.

    

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