Ectomycorrhizal-Dominated Boreal and Tropical Forests Have Distinct Fungal Communities, but Analogous Spatial Patterns across Soil Horizons

Fungi regulate key nutrient cycling processes in many forest ecosystems, but their diversity and distribution within and across ecosystems are poorly understood. Here, we examine the spatial distribution of fungi across a boreal and tropical ecosystem, focusing on ectomycorrhizal fungi. We analyzed fungal community composition across litter (organic horizons) and underlying soil horizons (0–20 cm) using 454 pyrosequencing and clone library sequencing. In both forests, we found significant clustering of fungal communities by site and soil horizons with analogous patterns detected by both sequencing technologies. Free-living saprotrophic fungi dominated the recently-shed leaf litter and ectomycorrhizal fungi dominated the underlying soil horizons. This vertical pattern of fungal segregation has also been found in temperate and European boreal forests, suggesting that these results apply broadly to ectomycorrhizal-dominated systems, including tropical rain forests. Since ectomycorrhizal and free-living saprotrophic fungi have different influences on soil carbon and nitrogen dynamics, information on the spatial distribution of these functional groups will improve our understanding of forest nutrient cycling

Contrasting environmental preferences of photosynthetic and non‐photosynthetic soil cyanobacteria across the globe

Aim: Cyanobacteria have shaped the history of life on Earth and continue to play important roles as carbon and nitrogen fixers in terrestrial ecosystems. However, their global distribution and ecological preferences remain poorly understood, particularly for two recently discovered non‐photosynthetic cyanobacterial classes (Sericytochromatia and Melainabacteria). Location: Two hundred and thirty‐seven locations across six continents encompassing multiple climates (arid, temperate, tropical, continental and polar) and vegetation types (forests, grasslands and shrublands). Time period: Sampling was carried out between 2003 and 2015. Major taxa studied: Photosynthetic and non‐photosynthetic cyanobacterial taxa. Methods: We conducted a field survey and used co‐occurrence network analysis and structural equation modelling to evaluate the distribution and environmental preferences of soil cyanobacteria across the globe. These ecological preferences were used to create a global atlas (predictive distribution maps) of soil cyanobacteria. Results: Network analyses identified three major groups of cyanobacterial taxa, which resembled the three main cyanobacterial classes: the photosynthetic Oxyphotobacteria‐dominated cluster, which were prevalent in arid and semi‐arid areas, and the non‐photosynthetic Sericytochromatia‐ and Melainabacteria‐dominated clusters, which preferred hyper‐arid oligotrophic and acidic/humid environments, respectively. Main conclusions: This study provides new insights into the environmental preferences of non‐photosynthetic cyanobacteria in soils globally. Our findings highlight the contrasting environmental preferences among the three clusters of cyanobacteria and suggest that alterations in environmental conditions linked to climate change might result in important changes in the ecology and biogeography of these functionally important microorganisms.M.D.-B. is supported by a Ramón y Cajal grant from the Spanish Ministry of Science and Innovation (RYC2018-025483-I), and by the BES grant agreement No LRB17\1019 (MUSGONET). The work of C.C.-D. and F.T.M. and the global drylands database were supported by the European Research Council [ERC Grant Agreements 242658 (BIOCOM) and 647038 (BIODESERT)] and by the Spanish Ministry of Economy and Competitiveness (BIOMOD project, ref. CGL2013-44661-R). F.T.M. acknowledges support from Generalitat Valenciana (BIOMORES project, ref. CIDEGENT/2018/041). Research on biodiversity by B.K.S. is supported by the Australian Research Council (DP170104634). R.D.B. was supported by the U.K. Department of Environment, Food and Rural Affairs (DEFRA) project no. BD5003 and a Biotechnology and Biological Sciences Research Council (BBSRC) International Exchange Grant (BB/L026406/1)

The emerging contribution of social wasps to grape rot disease ecology

Grape sour (bunch) rot is a polymicrobial disease of vineyards that causes millions of dollars in lost revenue per year due to decreased quality of grapes and resultant wine. The disease is associated with damaged berries infected with a community of acetic acid bacteria, yeasts, and filamentous fungi that results in rotting berries with high amounts of undesirable volatile acidity. Many insect species cause the initial grape berry damage that can lead to this disease, but most studies have focused on the role of fruit flies in facilitating symptoms and vectoring the microorganisms of this disease complex. Like fruit flies, social wasps are abundant in vineyards where they feed on ripe berries and cause significant damage, while also dispersing yeasts involved in wine fermentation. Despite this, their possible role in disease facilitation and dispersal of grape rots has not been explored. We tested the hypothesis that the paper wasp Polistes dominulus could facilitate grape sour rot in the absence of other insect vectors. Using marker gene sequencing we characterized the bacterial and fungal community of wild-caught adults. We used a sterilized foraging arena to determine if these wasps transfer viable microorganisms when foraging. We then tested if wasps harboring their native microbial community, or those inoculated with sour rot, had an effect on grape sour rot incidence and severity using a laboratory foraging arena. We found that all wasps harbor some portion of the sour rot microbial community and that they have the ability to transfer viable microorganisms when foraging. Foraging by inoculated and uninoculated wasps led to an increase in berry rot disease symptom severity and incidence. Our results indicate that paper wasps can facilitate sour rot diseases in the absence of other vectors and that the mechanism of this facilitation may include both increasing host susceptibility and transmitting these microbial communities to the grapes. Social wasps are understudied but relevant players in the sour rot ecology of vineyards

Forensic analysis of the microbiome of phones and shoes

BACKGROUND: Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. RESULTS: Samples taken from different surface types maintained significantly different microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space. CONCLUSIONS: Correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-015-0082-9) contains supplementary material, which is available to authorized users

Exploring the boundaries of microbial habitability in soil

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dragone, N. B., Diaz, M. A., Hogg, I., Lyons, W. B., Jackson, W. A., Wall, D. H., Adams, B. J., & Fierer, N. Exploring the boundaries of microbial habitability in soil. Journal of Geophysical Research: Biogeosciences, 126(6), (2021): e2020JG006052, https://doi.org/10.1029/2020JG006052.Microbes are widely assumed to be capable of colonizing even the most challenging terrestrial surface environments on Earth given enough time. We would not expect to find surface soils uninhabited by microbes as soils typically harbor diverse microbial communities and viable microbes have been detected in soils exposed to even the most inhospitable conditions. However, if uninhabited soils do exist, we might expect to find them in Antarctica. We analyzed 204 ice-free soils collected from across a remote valley in the Transantarctic Mountains (84–85°S, 174–177°W) and were able to identify a potential limit of microbial habitability. While most of the soils we tested contained diverse microbial communities, with fungi being particularly ubiquitous, microbes could not be detected in many of the driest, higher elevation soils—results that were confirmed using cultivation-dependent, cultivation-independent, and metabolic assays. While we cannot confirm that this subset of soils is completely sterile and devoid of microbial life, our results suggest that microbial life is severely restricted in the coldest, driest, and saltiest Antarctic soils. Constant exposure to these conditions for thousands of years has limited microbial communities so that their presence and activity is below detectable limits using a variety of standard methods. Such soils are unlikely to be unique to the studied region with this work supporting previous hypotheses that microbial habitability is constrained by near-continuous exposure to cold, dry, and salty conditions, establishing the environmental conditions that limit microbial life in terrestrial surface soils.This work was supported by grants from the U.S. National Science Foundation (ANT 1341629 to B. J. Adams, N. Fierer, W. Berry Lyons, and D. H. Wall and OPP 1637708 to B. J. Adams) with additional support provided to N. B. Dragone from University Colorado Department of Ecology and Evolutionary Biology

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions

Microbial Biogeography of Public Restroom Surfaces

We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, the diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited by bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing of the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla: Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with hands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floor surfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associated bacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were more common in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in female restrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomic observations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate that restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear linkages between communities on or in different body sites and those communities found on restroom surfaces. More generally, this work is relevant to the public health field as we show that human-associated microbes are commonly found on restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching of surfaces. Furthermore, we demonstrate that we can use high-throughput analyses of bacterial communities to determine sources of bacteria on indoor surfaces, an approach which could be used to track pathogen transmission and test the efficacy of hygiene practices

Elevational constraints on the composition and genomic attributes of microbial communities in Antarctic soils

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dragone, N. B., Henley, J. B., Holland-Moritz, H., Diaz, M., Hogg, I. D., Lyons, W. B., Wall, D. H., Adams, B. J., & Fierer, N. Elevational constraints on the composition and genomic attributes of microbial communities in Antarctic soils. Msystems, 7(1), (2022): e01330-21, https://doi.org/10.1128/msystems.01330-21.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.Geospatial support for this work was provided by the Polar Geospatial Center under NSF-OPP awards 1043681 and 155969. This work was supported by grants from the U.S. National Science Foundation Office of Polar Programs (1341629, 1341629, 1341736, and 1637708 to B.J.A., N.F., W.B.L., and D.H.W.), with additional support provided to N.B.D. from the University of Colorado Department of Ecology and Evolutionary Biology