The use of different 16S rRNA gene variable regions in biogeographical studies.

16S rRNA gene amplicon sequencing is routinely used in environmental surveys to identify microbial diversity and composition of the samples of interest. The dominant sequencing technology of the past decade (Illumina) is based on the sequencing of 16S rRNA hypervariable regions. Online sequence data repositories, which represent an invaluable resource for investigating microbial distributional patterns across spatial, environmental or temporal scales, contain amplicon datasets from diverse 16S rRNA gene variable regions. However, the utility of these sequence datasets is potentially reduced by the use of different 16S rRNA gene amplified regions. By comparing 10 Antarctic soil samples sequenced for five different 16S rRNA amplicons, we explore whether sequence data derived from diverse 16S rRNA variable regions can be validly used as a resource for biogeographical studies. Patterns of shared and unique taxa differed among samples as a result of variable taxonomic resolutions of the assessed 16S rRNA variable regions. However, our analyses also suggest that the use of multi-primer datasets for biogeographical studies of the domain Bacteria is a valid approach to explore bacterial biogeographical patterns due to the preservation of bacterial taxonomic and diversity patterns across different variable region datasets. We deem composite datasets useful for biogeographical studies.Gilda Varliero, Pedro H. Lebre, Mark I. Stevens, Paul Czechowski, Thulani Makhalanyane, Don A. Cowa

Structural characterization and directed evolution of a novel acetyl xylan esterase reveals thermostability determinants of the carbohydrate esterase 7 family

Please read abstract in the article.The South Africa Bio-catalysis Initiative, Department of Science and Technology, the University of Pretoria Genomics Research Institute (D.A.C. and T.P.M.), the National Research Foundation (W.-D.S. and B.T.S.), the Research Development Program (T.P.M. and S.V.), and the Organization for Women in Science in the Developing World (OWSD) (F.A.A.).http://aem.asm.org2018-10-01hj2018BiochemistryGenetic

The global distribution and environmental drivers of the soil antibiotic resistome

DATA AVAILABILITY : All the materials, raw data, and protocols used in the article are available upon request and without restriction. The data used in this article are available from Figshare (https:// figsh are. com/s/ 5640a 4e375 272e4 eebf1).ADDITIONAL FILE 1: SUPPLEMENTARY FIGURE 1. Extrapolation of uncertainties associated with the global survey used in this study. SUPPLEMENTARY FIGURE 2. Main structure for the a priori structural equation model used in this study. SUPPLEMENTARY FIGURE 3. Structural equation models assessing the direct and indirect effects of environmental factors on the proportion (A) and richness (B) of ARGs in natural ecosystems only (i.e. croplands excluded, n = 802). SUPPLEMENTARY FIGURE 4. Global precipitation (A) and temperature (B) seasonality maps used in our study (https:// www. world clim. org/ data/ index. html). SUPPLEMENTARY TABLE 1. List of antibiotic resistance genes (ARGs) mobile genetic elements (MGEs) considered in this study. SUPPLEMENTARY TABLE 2. Biomes included in this study. The biome classification was done based on vegetation field information and climatic information from the Köppen classification16. SUPPLEMENTARY TABLE 3. Environmental factors included in our structural equation model. SUPPLEMENTARY TABLE 4. Standardized direct effects of SEM on the proportion of soil ARGs. SUPPLEMENTARY TABLE 5. Standardized direct effects of SEM on the richness of soil ARGs.BACKGROUND : Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth’s largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs. RESULTS : We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. CONCLUSIONS : Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome.The European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant, a Large Research Grant from the British Ecological Society, the European Research Council, a Ramón y Cajal grant, the Spanish Ministry of Science and Innovation, a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía, Generalitat Valenciana, Australian Research Council, the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation and Slovenian Research Agency.https://microbiomejournal.biomedcentral.comam2023BiochemistryGeneticsMicrobiology and Plant Patholog

Biogeographical survey of soil microbiomes across sub-Saharan Africa:structure, drivers, and predicted climate-driven changes

BACKGROUND: Top-soil microbiomes make a vital contribution to the Earth’s ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents. RESULTS: The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa’s top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation. CONCLUSION: This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-022-01297-w

The global distribution and environmental drivers of the soil antibiotic resistome

Background: Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth’s largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs. Results: We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. Conclusions: Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome.This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement 702057 (CLIMIFUN), a Large Research Grant from the British Ecological Society (agreement no. LRA17\1193; MUSGONET), and from the European Research Council (ERC grant agreement no. 647038, BIODESERT). M. D. B. was also supported by a Ramón y Cajal grant (RYC2018-025483-I). M.D-B. also acknowledges support from the Spanish Ministry of Science and Innovation for the I+D+i project PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033. M.D-B. is also supported by a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014-2020 Objetivo temático “01 - Refuerzo de la investigación, el desarrollo tecnológico y la innovación”) associated with the research project P20_00879 (ANDABIOMA). FTM acknowledges support from Generalitat Valenciana (CIDEGENT/2018/041). J. Z. H and H. W. H. are financially supported by Australian Research Council (DP210100332). We also thank the project CTM2015-64728-C2-2-R from the Ministry of Science of Spain. C. A. G. and N. E. acknowledge funding by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation (FZT 118). TG was financially supported by Slovenian Research Agency (P4-0107, J4-3098 and J4-4547)

The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence

In mature soils, plant species and soil type determine the selection of root microbiota. Which of these two factors drives rhizosphere selection in barren substrates of developing desert soils has, however, not yet been established. Chronosequences of glacier forelands provide ideal natural environments to identify primary rhizosphere selection factors along the changing edaphic conditions of a developing soil. Here, we analyze changes in bacterial diversity in bulk soils and rhizospheres of a pioneer plant across a High Arctic glacier chronosequence. We show that the developmental stage of soil strongly modulates rhizosphere community assembly, even though plant-induced selection buffers the effect of changing edaphic factors. Bulk and rhizosphere soils host distinct bacterial communities that differentially vary along the chronosequence. Cation exchange capacity, exchangeable potassium, and metabolite concentration in the soil account for the rhizosphere bacterial diversity. Although the soil fraction (bulk soil and rhizosphere) explains up to 17.2% of the variation in bacterial microbiota, the soil developmental stage explains up to 47.7% of this variation. In addition, the operational taxonomic unit (OTU) co-occurrence network of the rhizosphere, whose complexity increases along the chronosequence, is loosely structured in barren compared with mature soils, corroborating our hypothesis that soil development tunes the rhizosphere effect

Author correction : roadmap for naming uncultivated archaea and bacteria

Correction to: Nature Microbiology https://doi.org/10.1038/s41564-020-0733-x , published online 8 June 2020. In the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online

Roadmap for naming uncultivated Archaea and Bacteria

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity

Draft Genome Sequence of Williamsia sp. Strain D3, Isolated From the Darwin Mountains, Antarctica

Actinobacteria are the dominant taxa in Antarctic desert soils. Here, we describe the first draft genome of a member of the genus Williamsia (strain D3) isolated from Antarctic soil. The genome of this psychrotolerant bacterium may help to elucidate crucial survival mechanisms for organisms inhabiting cold desert soil systems.Fil: Guerrero, Leandro Demián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of Pretoria; Nueva ZelandaFil: Makhalanyane, T. P.. University of Pretoria; Nueva ZelandaFil: Aislabie, J. M.. University of Pretoria; Nueva ZelandaFil: Cowan, D. A.. University of Pretoria; Nueva Zeland