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  1. ABSTRACT There are complex interactions between an organism's microbiome and its response to stressors, often referred to as the ‘gut–brain axis’; however, the ecological relevance of this axis in wild animals remains poorly understood. Here, we used a chronic mild stress protocol to induce stress in wild-caught house sparrows (Passer domesticus), and compared microbial communities among stressed animals, those recovering from stress, captive controls (unstressed) and a group not brought into captivity. We assessed changes in microbial communities and abundance of shed microbes by culturing cloacal samples on multiple media to select for aerobic and anaerobic bacteria and fungi. We complemented this with cultivation-independent 16S and ITS rRNA gene amplification and sequencing, pairing these results with host physiological and immune metrics, including body mass change, relative spleen mass and plasma corticosterone concentrations. We found significant effects of stress and captivity on the house sparrow microbiomes, with stress leading to an increased relative abundance of endotoxin-producing bacteria – a possible mechanism for the hyperinflammatory response observed in captive avians. While we found evidence that the microbiome community partially recovers after stress cessation, animals may lose key taxa, and the abundance of endotoxin-producing bacteria persists. Our results suggest an overall link betweenmore »chronic stress, host immune system and the microbiome, with the loss of potentially beneficial taxa (e.g. lactic acid bacteria), and an increase in endotoxin-producing bacteria due to stress and captivity. Ultimately, consideration of the host's microbiome may be useful when evaluating the impact of stressors on individual and population health.« less
    Free, publicly-accessible full text available April 1, 2023
  2. Mackelprang, Rachel (Ed.)
    ABSTRACT The inland soils found on the Antarctic continent represent one of the more challenging environments for microbial life on Earth. Nevertheless, Antarctic soils harbor unique bacterial and archaeal (prokaryotic) communities able to cope with extremely cold and dry conditions. These communities are not homogeneous, and the taxonomic composition and functional capabilities (genomic attributes) of these communities across environmental gradients remain largely undetermined. We analyzed the prokaryotic communities in soil samples collected from across the Shackleton Glacier region of Antarctica by coupling quantitative PCR, marker gene amplicon sequencing, and shotgun metagenomic sequencing. We found that elevation was the dominant factor explaining differences in the structures of the soil prokaryotic communities, with the drier and saltier soils found at higher elevations harboring less diverse communities and unique assemblages of cooccurring taxa. The higher-elevation soil communities also had lower maximum potential growth rates (as inferred from metagenome-based estimates of codon usage bias) and an overrepresentation of genes associated with trace gas metabolism. Together, these results highlight the utility of assessing community shifts across pronounced environmental gradients to improve our understanding of the microbial diversity found in Antarctic soils and the strategies used by soil microbes to persist at the limits of habitability.more »IMPORTANCE Antarctic soils represent an ideal system to study how environmental properties shape the taxonomic and functional diversity of microbial communities given the relatively low diversity of Antarctic soil microbial communities and the pronounced environmental gradients that occur across soils located in reasonable proximity to one another. Moreover, the challenging environmental conditions typical of most Antarctic soils present an opportunity to investigate the traits that allow soil microbes to persist in some of the most inhospitable habitats on Earth. We used cultivation-independent methods to study the bacterial and archaeal communities found in soil samples collected from across the Shackleton Glacier region of the Transantarctic Mountains. We show that those environmental characteristics associated with elevation have the greatest impact on the structure of these microbial communities, with the colder, drier, and saltier soils found at higher elevations sustaining less diverse communities that were distinct from those in more hospitable soils with respect to their composition, genomic attributes, and overall life-history strategies. Notably, the harsher conditions found in higher-elevation soils likely select for taxa with lower maximum potential growth rates and an increased reliance on trace gas metabolism to support growth.« less
    Free, publicly-accessible full text available February 22, 2023
  3. Free, publicly-accessible full text available January 1, 2023
  4. Abstract Background Mosses in high-latitude ecosystems harbor diverse bacterial taxa, including N 2 -fixers which are key contributors to nitrogen dynamics in these systems. Yet the relative importance of moss host species, and environmental factors, in structuring these microbial communities and their N 2 -fixing potential remains unclear. We studied 26 boreal and tundra moss species across 24 sites in Alaska, USA, from 61 to 69° N. We used cultivation-independent approaches to characterize the variation in moss-associated bacterial communities as a function of host species identity and site characteristics. We also measured N 2 -fixation rates via 15 N 2 isotopic enrichment and identified potential N 2 -fixing bacteria using available literature and genomic information. Results Host species identity and host evolutionary history were both highly predictive of moss microbiome composition, highlighting strong phylogenetic coherence in these microbial communities. Although less important, light availability and temperature also influenced composition of the moss microbiome. Finally, we identified putative N 2 -fixing bacteria specific to some moss hosts, including potential N 2 -fixing bacteria outside well-studied cyanobacterial clades. Conclusions The strong effect of host identity on moss-associated bacterial communities demonstrates mosses’ utility for understanding plant-microbe interactions in non-leguminous systems. Our work alsomore »highlights the likely importance of novel bacterial taxa to N 2 -fixation in high-latitude ecosystems.« less
  5. Abstract Ecosystems across the globe receive elevated inputs of nutrients, but the consequences of this for soil fungal guilds that mediate key ecosystem functions remain unclear. We find that nitrogen and phosphorus addition to 25 grasslands distributed across four continents promotes the relative abundance of fungal pathogens, suppresses mutualists, but does not affect saprotrophs. Structural equation models suggest that responses are often indirect and primarily mediated by nutrient-induced shifts in plant communities. Nutrient addition also reduces co-occurrences within and among fungal guilds, which could have important consequences for belowground interactions. Focusing only on plots that received no nutrient addition, soil properties influence pathogen abundance globally, whereas plant community characteristics influence mutualists, and climate influence saprotrophs. We show consistent, guild-level responses that enhance our ability to predict shifts in soil function related to anthropogenic eutrophication, which can have longer-term consequences for plant communities.
  6. 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
  7. Abstract. Outlet glaciers that flow through the Transantarctic Mountains (TAM) experienced changes in ice thickness greater than other coastal regions of Antarctica during glacial maxima. As a result, ice-free areas that are currently exposed may have been covered by ice at various points during the Cenozoic, complicating our understanding of ecological succession in TAM soils. Our knowledge of glacial extent on small spatial scales is limited for the TAM, and studies of soil exposure duration and disturbance, in particular, are rare. We collected surface soil samples and, in some places, depth profiles every 5 cm to refusal (up to 30 cm) from 11ice-free areas along Shackleton Glacier, a major outlet glacier of the EastAntarctic Ice Sheet. We explored the relationship between meteoric 10Be and NO3- in these soils as a tool for understanding landscape disturbance and wetting history and as exposure proxies. Concentrations of meteoric 10Be spanned more than an order of magnitude across the region (2.9×108 to 73×108 atoms g−1) and are among the highest measured in polar regions. The concentrations of NO3- were similarly variable and ranged from ∼1 µg g−1 to 15 mg g−1. In examining differences and similarities in the concentrations of 10Be and NO3- with depth, we suggest that much of the southern portion of themore »Shackleton Glacier region has likely developed under a hyper-arid climate regime with minimal disturbance. Finally, we inferred exposure time using 10Be concentrations. This analysis indicates that the soils we analyzed likelyrange from recent exposure (following the Last Glacial Maximum) to possibly>6 Myr. We suggest that further testing and interrogation of meteoric 10Be and NO3- concentrations and relationships in soils can provide important information regarding landscape development, soil evolution processes, and inferred exposure durations of surfaces in the TAM.« less
  8. Sourdough bread is an ancient fermented food that has sustained humans around the world for thousands of years. It is made from a sourdough ‘starter culture’ which is maintained, portioned, and shared among bread bakers around the world. The starter culture contains a community of microbes made up of yeasts and bacteria, which ferment the carbohydrates in flour and produce the carbon dioxide gas that makes the bread dough rise before baking. The different acids and enzymes produced by the microbial culture affect the bread’s flavor, texture and shelf life. However, for such a dependable staple, sourdough bread cultures and the mixture of microbes they contain have scarcely been characterized. Previous studies have looked at the composition of starter cultures from regions within Europe. But there has never been a comprehensive study of how the microbial diversity of sourdough starters varies across and between continents. To investigate this, Landis, Oliverio et al. used genetic sequencing to characterize the microbial communities of sourdough starters from the homes of 500 bread bakers in North America, Europe and Australasia. Bread makers often think their bread’s unique qualities are due to the local environment of where the sourdough starter was made. However, Landis, Oliveriomore »et al. found that geographical location did not correlate with the diversity of the starter cultures studied. The data revealed that a group of microbes called acetic acid bacteria, which had been overlooked in past research, were relatively common in starter cultures. Moreover, starters with a greater abundance of this group of bacteria produced bread with a strong vinegar aroma and caused dough to rise at a slower rate. This research demonstrates which species of bacteria and yeast are most commonly found in sourdough starters, and suggests geographical location has little influence on the microbial diversity of these cultures. Instead, the diversity of microbes likely depends more on how the starter culture was made and how it is maintained over time.« less
  9. Moss-associated N2 fixation provides a substantial but heterogeneous input of new N to nutrient-limited ecosystems at high latitudes. In spite of the broad diversity of mosses found in boreal and Arctic ecosystems, the extent to which host moss identity drives variation in N2 fixation rates remains largely undetermined. We used 15N2 incubations to quantify the fixation rates associated with 34 moss species from 24 sites ranging from 60° to 68° N in Alaska, USA. Remarkably, all sampled moss genera fixed N2, including well-studied feather and peat mosses and genera such as Tomentypnum, Dicranum, and Polytrichum. The total moss-associated N2 fixation rates ranged from almost zero to 3.2 mg N m−2 d−1, with an average of 0.8 mg N m−2 d−1, based on abundance-weighted averages of all mosses summed for each site. Random forest models indicated that moss taxonomic family was a better predictor of rate variation across Alaska than any of the measured environmental factors, including site, pH, tree density, and mean annual precipitation and temperature. Consistent with this finding, mixed models showed that trends in N2 fixation rates among moss genera were consistent across biomes. We also found “hotspots” of high fixation rates in one-fourth of sampled sites. Ourmore »results demonstrated the importance of moss identity in influencing N2 fixation rates. This in turn indicates the potential utility of moss identity when making ecosystem N input predictions and exploring other sources of process rate variation.« less