Environmental Microbiome最新文献

{"title":"New fungal primers reveal the diversity of Mucoromycotinian arbuscular mycorrhizal fungi and their response to nitrogen application","authors":"Mirjam Seeliger, Sally Hilton, George Muscatt, Christopher Walker, David Bass, Felipe Albornoz, Rachel J. Standish, Neil D. Gray, Louis Mercy, Leonidas Rempelos, Carolin Schneider, Megan H. Ryan, Paul E. Bilsborrow, Gary D. Bending","doi":"10.1186/s40793-024-00617-x","DOIUrl":"https://doi.org/10.1186/s40793-024-00617-x","url":null,"abstract":"Arbuscular mycorrhizas (AM) are the most widespread terrestrial symbiosis and are both a key determinant of plant health and a major contributor to ecosystem processes through their role in biogeochemical cycling. Until recently, it was assumed that the fungi which form AM comprise the subphylum Glomeromycotina (G-AMF), and our understanding of the diversity and ecosystem roles of AM is based almost exclusively on this group. However recent evidence shows that fungi which form the distinctive 'fine root endophyte’ (FRE) AM morphotype are members of the subphylum Mucoromycotina (M-AMF), so that AM symbioses are actually formed by two distinct groups of fungi. We investigated the influence of nitrogen (N) addition and wheat variety on the assembly of AM communities under field conditions. Visual assessment of roots showed co-occurrence of G-AMF and M-AMF, providing an opportunity to compare the responses of these two groups. Existing ‘AM’ 18S rRNA primers which co-amplify G-AMF and M-AMF were modified to reduce bias against Mucoromycotina, and compared against a new ‘FRE’ primer set which selectively amplifies Mucoromycotina. Using the AM-primers, no significant effect of either N-addition or wheat variety on G-AMF or M-AMF diversity or community composition was detected. In contrast, using the FRE-primers, N-addition was shown to reduce M-AMF diversity and altered community composition. The ASV which responded to N-addition were closely related, demonstrating a clear phylogenetic signal which was identified only by the new FRE-primers. The most abundant Mucoromycotina sequences we detected belonged to the same Endogonales clades as dominant sequences associated with FRE morphology in Australia, indicating that closely related M-AMF may be globally distributed. The results demonstrate the need to consider both G-AMF and M-AMF when investigating AM communities, and highlight the importance of primer choice when investigating AMF community dynamics.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches","authors":"Esteban Góngora, Antoine-O. Lirette, Nastasia J. Freyria, Charles W. Greer, Lyle G. Whyte","doi":"10.1186/s40793-024-00616-y","DOIUrl":"https://doi.org/10.1186/s40793-024-00616-y","url":null,"abstract":"Decreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes. We observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8 ± 34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7 ± 12.3 HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources. These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches. Our metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Survival strategies of aerobic methanotrophs under hypoxia in methanogenic lake sediments","authors":"Almog Gafni, Maxim Rubin-Blum, Colin Murrell, Hanni Vigderovich, Werner Eckert, Nasmille Larke-Mejía, Orit Sivan","doi":"10.1186/s40793-024-00609-x","DOIUrl":"https://doi.org/10.1186/s40793-024-00609-x","url":null,"abstract":"<p><b>Correction: Environmental Microbiome (2024) 19:44 </b><b>https://doi.org/10.1186/s40793-024-00586-1</b></p><p>Following publication of the original article, the following three concerns were brought to the attention of the authors: Figure 4 was low resolution and, as a result, difficult to read; affiliation ‘6’ (see the original article) was missing from the affiliations of the second author, Maxim Rubin-Blum; the given and family names of the first author, Almog Gafni, were the wrong way around. These errors have since been corrected in the published article. The authors thank you for reading this erratum and apologize for any inconvenience caused.</p><h3>Authors and Affiliations</h3><ol><li><p>Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel</p><p>Almog Gafni, Hanni Vigderovich & Orit Sivan</p></li><li><p>Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel</p><p>Maxim Rubin-Blum</p></li><li><p>School of Environmental Sciences, University of East Anglia, Norwich, UK</p><p>Colin Murrell</p></li><li><p>The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel</p><p>Werner Eckert</p></li><li><p>Quadram Institute Bioscience, Norwich Research Park, Norwich, UK</p><p>Nasmille Larke-Mejía</p></li><li><p>Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel</p><p>Maxim Rubin-Blum</p></li></ol><span>Authors</span><ol><li><span>Almog Gafni</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Maxim Rubin-Blum</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Colin Murrell</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Hanni Vigderovich</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Werner Eckert</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Nasmille Larke-Mejía</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Orit Sivan</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li></ol><h3>Corresponding author</h3><p>Correspondence to Almog Gafni.</p><h3>Publisher's Note</h3><p>Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.</p><p>Article corrected in 2024.</p><p><b>Open Access</b> This article is licensed under a Creative Commons Attribution 4.0 International L","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impacts of ecological disturbances on the diversity of biosynthetic gene clusters in kauri (Agathis australis) soil","authors":"Alexa K. Byers, Nick Waipara, Leo Condron, Amanda Black","doi":"10.1186/s40793-024-00613-1","DOIUrl":"https://doi.org/10.1186/s40793-024-00613-1","url":null,"abstract":"The ancient kauri (Agathis australis) dominated forests of Aotearoa New Zealand are under threat from a multitude of ecological disturbances such as forest fragmentation, biodiversity loss, climate change, and the spread of the virulent soil pathogen Phytophthora agathidicida. Taking a wider ecosystem-level approach, our research aimed to explore the impacts of forest disturbance and disease outbreaks on the biosynthetic potential and taxonomic diversity of the kauri soil microbiome. We explored the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in soils from a range of kauri forests that varied according to historical disturbance and dieback expression. To characterise the diversity of microbial BGCs, we targeted the non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene regions for sequencing using long-read PacBio® HiFi sequencing. Furthermore, the soil bacterial and fungal communities of each forest were characterized using 16 S rRNA and ITS gene region sequencing. We identified a diverse array of naturally occurring microbial BGCs in the kauri forest soils, which may offer promising targets for the exploration of secondary metabolites with anti-microbial activity against P. agathidicida. We detected differences in the number and diversity of microbial BGCs according to forest disturbance history. Notably, soils associated with the most undisturbed kauri forest had a higher number and diversity of microbial NRPS-type BGCs, which may serve as a potential indicator of natural levels of microbiome resistance to pathogen invasion. By linking patterns in microbial biosynthetic diversity to forest disturbance history, this research highlights the need for us to consider the influence of ecological disturbances in potentially predisposing forests to disease by impacting the wider health of forest soil ecosystems. Furthermore, by identifying the range of microbial BGCs present at a naturally high abundance in kauri soils, this research contributes to the future discovery of natural microbial compounds that may potentially enhance the disease resilience of kauri forests. The methodological approaches used in this study highlight the value of moving beyond a taxonomic lens when examining the response of microbial communities to ecosystem disturbance and the need to develop more functional measures of microbial community resilience to invasive plant pathogens.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Individual methanogenic granules are whole-ecosystem replicates with reproducible responses to environmental cues","authors":"Anna Trego, Sarah O’Sullivan, Vincent O’Flaherty, Gavin Collins, Umer Zeeshan Ijaz","doi":"10.1186/s40793-024-00615-z","DOIUrl":"https://doi.org/10.1186/s40793-024-00615-z","url":null,"abstract":"In this study, individual methanogenic (anaerobic), granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates were sourced from a lab-scale, engineered, biological wastewater treatment system, were size-separated, and the largest granules were individually subjected to controlled environmental cues in micro-batch reactors (μBRs). Individual granules were identical with respect to the structure of the active community based on cDNA analysis. Additionally, it was observed that the active microbial community of individual granules, at the depth of 16S rRNA gene sequencing, produced reproducible responses to environmental changes in pH, temperature, substrate, and trace-metal supplementation. We identified resilient and susceptible taxa associated with each environmental condition tested, as well as selected specialists, whose niche preferences span the entire trophic chain required for the complete anaerobic degradation of organic matter. We found that single anaerobic granules can be considered highly-replicated whole-ecosystems with potential usefulness for the field of microbial ecology. Additionally, they act as the smallest whole-community unit within the meta-community of an engineered bioreactor. When subjected to various environmental cues, anaerobic granules responded reproducibly allowing for rare or unique opportunities for high-throughput studies testing whole-community responses to a wide range of environmental conditions.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-centric metagenomes unveiling the hidden resistome in an anchialine cave","authors":"Tanja Vojvoda Zeljko, Katarina Kajan, Branko Jalžić, Anyi Hu, Neven Cukrov, Marija Marguš, Nuša Cukrov, Tamara Marković, Raffaella Sabatino, Andrea Di Cesare, Sandi Orlić","doi":"10.1186/s40793-024-00612-2","DOIUrl":"https://doi.org/10.1186/s40793-024-00612-2","url":null,"abstract":"Antibiotic resistance is a critical global concern, posing significant challenges to human health and medical treatments. Studying antibiotic resistance genes (ARGs) is essential not only in clinical settings but also in diverse environmental contexts. However, ARGs in unique environments such as anchialine caves, which connect both fresh and marine water, remain largely unexplored despite their intriguing ecological characteristics. We present the first study that comprehensively explores the occurrence and distribution of ARGs and mobile genetic elements (MGEs) within an anchialine cave. Utilizing metagenomic sequencing we uncovered a wide array of ARGs with the bacitracin resistance gene, bacA and multidrug resistance genes, being the most dominant. The cave’s microbial community and associated resistome were significantly influenced by the salinity gradient. The discovery of novel β-lactamase variants revealed the cave’s potential as a reservoir for previously undetected resistance genes. ARGs in the cave demonstrated horizontal transfer potential via plasmids, unveiling ecological implications. These findings highlight the need for further exploration of the resistome in unique environments like anchialine caves. The interconnected dynamics of ARGs and MGEs within anchialine caves offer valuable insights into potential reservoirs and mechanisms of antibiotic resistance in natural ecosystems. This study not only advances our fundamental understanding but also highlights the need for a comprehensive approach to address antibiotic resistance in diverse ecological settings.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The herbicidal activity of pre-emergence herbicide cinmethylin and its potential risks on soil ecology: pH, enzyme activities and bacterial community.","authors":"Haiyan Yu, Hailan Cui, Jingchao Chen, Xiangju Li","doi":"10.1186/s40793-024-00608-y","DOIUrl":"10.1186/s40793-024-00608-y","url":null,"abstract":"<p><strong>Background: </strong>The herbicide cinmethylin, which was originally registered for use in rice fields, has the potential to control grass weeds in wheat fields before the emergence of wheat. However, its herbicidal activity against various troublesome grass weeds that infest wheat fields in China and its relationships with soil pH, soil enzymes and soil bacteria are not well known. Here, the effects of applying cinmethylin on the soil surface were tested on six grass weeds, and its impacts on soil characteristics, including the soil pH, soil enzymes and bacterial community, were evaluated.</p><p><strong>Results: </strong>Alopecurus aequalis, A. japonicus and A. myosuroides were highly sensitive to cinmethylin, with GR₅₀ values of 78.77, 61.49 and 119.67 g a.i. ha^- 1, respectively. The half-lives of cinmethylin at 1-, 10- and 100-fold the recommended rates were estimated at 26.46 - 52.33 d. Cinmethylin significantly increased the soil pH but decreased the activities of soil sucrase and urease. At 10- and 100-fold the recommended rate of cinmethylin, the bacterial abundance and diversity significantly decreased at 30 and 60 days after cinmethylin treatment. Cinmethylin at 100-fold the recommended rates largely promoted bacterial co-occurrence network complexity. Cinmethylin at high concentrations temporarily inhibited the abundance of the Nitrospira genus, as indicated by the copy numbers of the ammonia-oxidising archaea (AOA) amoA and ammonia-oxidising bacteria (AOB) amoA genes. Further analysis revealed that soil pH was negatively related to soil urease, and a significantly positive correlation was detected between soil urease and soil nitrification.</p><p><strong>Conclusion: </strong>Collectively, the application of cinmethylin at the recommended field dose had nearly no effect on the soil ecosystem, but its potential risks at high concentrations deserve further attention.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11382390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142156422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Networking the desert plant microbiome, bacterial and fungal symbionts structure and assortativity in co-occurrence networks.","authors":"Kenji Maurice, Liam Laurent-Webb, Amélia Bourceret, Stéphane Boivin, Hassan Boukcim, Marc-André Selosse, Marc Ducousso","doi":"10.1186/s40793-024-00610-4","DOIUrl":"10.1186/s40793-024-00610-4","url":null,"abstract":"<p><p>In nature, microbes do not thrive in seclusion but are involved in complex interactions within- and between-microbial kingdoms. Among these, symbiotic associations with mycorrhizal fungi and nitrogen-fixing bacteria are namely known to improve plant health, while providing resources to benefit other microbial members. Yet, it is not clear how these microbial symbionts interact with each other or how they impact the microbiota network architecture. We used an extensive co-occurrence network analysis, including rhizosphere and roots samples from six plant species in a natural desert in AlUla region (Kingdom of Saudi Arabia) and described how these symbionts were structured within the plant microbiota network. We found that the plant species was a significant driver of its microbiota composition and also of the specificity of its interactions in networks at the microbial taxa level. Despite this specificity, a motif was conserved across all networks, i.e., mycorrhizal fungi highly covaried with other mycorrhizal fungi, especially in plant roots-this pattern is known as assortativity. This structural property might reflect their ecological niche preference or their ability to opportunistically colonize roots of plant species considered non symbiotic e.g., H. salicornicum, an Amaranthaceae. Furthermore, these results are consistent with previous findings regarding the architecture of the gut microbiome network, where a high level of assortativity at the level of bacterial and fungal orders was also identified, suggesting the existence of general rules of microbiome assembly. Otherwise, the bacterial symbionts Rhizobiales and Frankiales covaried with other bacterial and fungal members, and were highly structural to the intra- and inter-kingdom networks. Our extensive co-occurrence network analysis of plant microbiota and study of symbiont assortativity, provided further evidence on the importance of bacterial and fungal symbionts in structuring the global plant microbiota network.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142120942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial core communities in activated sludge plants are strongly affected by immigration and geography.","authors":"Sofie Zacho Vestergaard, Giulia Dottorini, Miriam Peces, Admir Murguz, Morten Kam Dahl Dueholm, Marta Nierychlo, Per Halkjær Nielsen","doi":"10.1186/s40793-024-00604-2","DOIUrl":"https://doi.org/10.1186/s40793-024-00604-2","url":null,"abstract":"<p><strong>Background: </strong>The microbiota in wastewater treatment plants (WWTPs) and incoming wastewater is critical for the treatment process, the preservation of natural ecosystems and human health, and for the recovery of resources and achievement of sustainability goals. Both core species and conditionally rare and abundant taxa (CRAT) are considered process-critical but little is known about identity as well as true functional and ecological importance. Here, we present a comprehensive investigation of the microbiota of 84 municipal activated sludge (AS) plants with nutrient removal treating ~ 70% of all wastewater within a confined geographical area, Denmark (43,000 km²). With the use of an ecosystem-specific database (MiDAS 5.2), species-level classification allowed us to investigate the core and CRAT species, whether they were active, and important factors determining their presence.</p><p><strong>Results: </strong>We established a comprehensive catalog of species with names or placeholder names showing each plant contained approx. 2,500 different species. Core and CRAT represented in total 258 species, constituting around 50% of all reads in every plant. However, not all core and CRAT could be regarded as process-critical as growth rate calculations revealed that 43% did not grow in the AS plants and were present only because of continuous immigration from the influent. Analyses of regional microbiota differences and distance decay patterns revealed a stronger effect for species than genera, demonstrating that geography had a clear effect on the AS microbiota, even across a limited geographical area such as Denmark (43,000 km²).</p><p><strong>Conclusions: </strong>The study is the first comprehensive investigation of WWTPs in a confined geographical area providing new insights in our understanding of activated sludge microbiology by introducing a concept of combining immigration and growth calculation with identifying core and CRAT to reveal the true ecosystem-critical organisms. Additionally, the clear biogeographical pattern on this scale highlights the need for more region-level studies to find regional process-critical taxa (core and CRAT), especially at species and amplicon sequence variant (ASV) level.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11361056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ancestral environment of teosinte populations shapes their root microbiome.","authors":"Christopher J Barnes, Maria Sophie Bünner, M Rosario Ramírez-Flores, Ida Broman Nielsen, Jazmin Ramos-Madrigal, Daria Zharikova, Chloee M McLaughlin, M Thomas Gilbert, Ruairidh J H Sawers","doi":"10.1186/s40793-024-00606-0","DOIUrl":"https://doi.org/10.1186/s40793-024-00606-0","url":null,"abstract":"<p><strong>Background: </strong>The composition of the root microbiome affects the host's growth, with variation in the host genome associated with microbiome variation. However, it is not known whether this intra-specific variation of root microbiomes is a consequence of plants performing targeted manipulations of them to adapt to their local environment or varying passively with other traits. To explore the relationship between the genome, environment and microbiome, we sampled seeds from teosinte populations across its native range in Mexico. We then grew teosinte accessions alongside two modern maize lines in a common garden experiment. Metabarcoding was performed using universal bacterial and fungal primers to profile their root microbiomes.</p><p><strong>Results: </strong>The root microbiome varied between the two modern maize lines and the teosinte accessions. We further found that variation of the teosinte genome, the ancestral environment (temperature/elevation) and root microbiome were all correlated. Multiple microbial groups significantly varied in relative abundance with temperature/elevation, with an increased abundance of bacteria associated with cold tolerance found in teosinte accessions taken from high elevations.</p><p><strong>Conclusions: </strong>Our results suggest that variation in the root microbiome is pre-conditioned by the genome for the local environment (i.e. non-random). Ultimately, these claims would be strengthened by confirming that these differences in the root microbiome impact host phenotype, for example, by confirming that the root microbiomes of high-elevation teosinte populations enhance cold tolerance.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11363609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}