Environmental Microbiome最新文献

{"title":"Irradiance level and elevation shape the soil microbiome communities of Coffea arabica L.","authors":"Inocência da Piedade E Tapaça, Chinedu C Obieze, Gilberto V de Melo Pereira, David Fangueiro, João Coutinho, Irene Fraga, Fábio L Partelli, José C Ramalho, Isabel Marques, Ana I Ribeiro-Barros","doi":"10.1186/s40793-024-00619-9","DOIUrl":"https://doi.org/10.1186/s40793-024-00619-9","url":null,"abstract":"<p><strong>Background: </strong>The nexus plant-microbe-environment is essential to understand the ecosystem processes shaping plant health and fitness. Within this triangle, soils and associated microflora are among the key ecosystem's drivers, underpinning plant productivity and evolution. In this study, we conducted a comprehensive analysis (physicochemical properties, enzyme activities, and taxonomic diversity) of soils under the canopy projection of Coffea arabica trees along a gradient of elevation (600, 800, and 900 m) and shade (0, 50, 100%).</p><p><strong>Results: </strong>While shade had no influence on most parameters, altitude shaped the dynamics of microbial communities. Available phosphorus, soil organic carbon, and nitrate were significantly higher at 800 m, likely due to the higher activities of β-glucosidase and phosphatases at this altitude. Microbial biomass (carbon and nitrogen) and moisture were significantly higher at 600 and 900 m, which might be attributed to the abundance and richness of soil microorganisms. Indeed, metabarcoding analysis revealed a complex pattern of microbial consortia (bacteria, archaea, fungi) at the three altitudes, with the lowest index of richness recorded at 800 m. The highest number of Amplicon Sequence Variants was observed in bacteria, whose functional analysis revealed distinct metabolic adaptations across different altitudes. At 900 m, the main functional attributes favored the responses to environmental stimuli and microbial interactions; at 800 m, the predominant metabolic pathways were related to organic matter, fermentation, and bioremediation; and at the lower 600 m, the pathways shifted towards the breakdown of plant-derived compounds (e.g. geraniol, limonene, and pinene degradation).</p><p><strong>Conclusion: </strong>Overall, the results indicate a higher effectiveness of the microbial consortium at 800 m, which might result in better nutrient cycling. The study highlights the importance of canopy shade species and elevation for the composition of microbial consortia in C. arabica, unveiling ecological functions beyond plant health, with implications for bio-based solutions and biotechnology.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481607/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478100","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 interplay between host-specificity and habitat-filtering influences sea cucumber microbiota across an environmental gradient of pollution.","authors":"Sheena Suet-Wah Chung, Khan Cheung, Bovern Suchart Arromrak, Zhenzhen Li, Cham Man Tse, Juan Diego Gaitán-Espitia","doi":"10.1186/s40793-024-00620-2","DOIUrl":"https://doi.org/10.1186/s40793-024-00620-2","url":null,"abstract":"<p><p>Environmental gradients can influence morpho-physiological and life-history differences in natural populations. It is unclear, however, to what extent such gradients can also modulate phenotypic differences in other organismal characteristics such as the structure and function of host-associated microbial communities. In this work, we addressed this question by assessing intra-specific variation in the diversity, structure and function of environmental-associated (sediment and water) and animal-associated (skin and gut) microbiota along an environmental gradient of pollution in one of the most urbanized coastal areas in the world. Using the tropical sea cucumber Holothuria leucospilota, we tested the interplay between deterministic (e.g., environmental/host filtering) and stochastic (e.g., random microbial dispersal) processes underpinning host-microbiome interactions and microbial assemblages. Overall, our results indicate that microbial communities are complex and vary in structure and function between the environment and the animal hosts. However, these differences are modulated by the level of pollution across the gradient with marked clines in alpha and beta diversity. Yet, such clines and overall differences showed opposite directions when comparing environmental- and animal-associated microbial communities. In the sea cucumbers, intrinsic characteristics (e.g., body compartments, biochemistry composition, immune systems), may underpin the observed intra-individual differences in the associated microbiomes, and their divergence from the environmental source. Such regulation favours specific microbial functional pathways that may play an important role in the survival and physiology of the animal host, particularly in high polluted areas. These findings suggest that the interplay between both, environmental and host filtering underpins microbial community assembly in H. leucospilota along the pollution gradient in Hong Kong.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11479550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478102","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":"Genetic diversity, stress tolerance and phytobeneficial potential in rhizobacteria of Vachellia tortilis subsp. raddiana.","authors":"Mohamed Hnini, Jamal Aurag","doi":"10.1186/s40793-024-00611-3","DOIUrl":"https://doi.org/10.1186/s40793-024-00611-3","url":null,"abstract":"<p><strong>Background: </strong>Soil bacteria often form close associations with their host plants, particularly within the root compartment, playing a significant role in plant growth and stress resilience. Vachellia tortilis subsp. raddiana, (V. tortilis subsp. raddiana)a leguminous tree, naturally thrives in the harsh, arid climate of the Guelmim region in southern Morocco. This study aims to explore the diversity and potential plant growth-promoting (PGP) activities of bacteria associated with this tree.</p><p><strong>Results: </strong>A total of 152 bacterial isolates were obtained from the rhizosphere of V. tortilis subsp. raddiana. Rep-PCR fingerprinting revealed 25 distinct genomic groups, leading to the selection of 84 representative strains for further molecular identification via 16 S rRNA gene sequencing. Seventeen genera were identified, with Bacillus and Pseudomonas being predominant. Bacillus strains demonstrated significant tolerance to water stress (up to 30% PEG), while Pseudomonas strains showed high salinity tolerance (up to 14% NaCl). In vitro studies indicated variability in PGP activities among the strains, including mineral solubilization, biological nitrogen fixation, ACC deaminase activity, and production of auxin, siderophores, ammonia, lytic enzymes, and HCN. Three elite strains were selected for greenhouse inoculation trials with V. tortilis subsp. raddiana. Strain LMR725 notably enhanced various plant growth parameters compared to uninoculated control plants.</p><p><strong>Conclusions: </strong>The findings underscore the potential of Bacillus and Pseudomonas strains as biofertilizers, with strain LMR725 showing particular promise in enhancing the growth of V. tortilis subsp. raddiana. This strain emerges as a strong candidate for biofertilizer formulation aimed at improving plant growth and resilience in arid environments.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11438029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142356176","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":"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":"&lt;p&gt;&lt;b&gt;Correction: Environmental Microbiome (2024) 19:44 &lt;/b&gt;&lt;b&gt;https://doi.org/10.1186/s40793-024-00586-1&lt;/b&gt;&lt;/p&gt;&lt;p&gt;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.&lt;/p&gt;&lt;h3&gt;Authors and Affiliations&lt;/h3&gt;&lt;ol&gt;&lt;li&gt;&lt;p&gt;Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel&lt;/p&gt;&lt;p&gt;Almog Gafni, Hanni Vigderovich &amp; Orit Sivan&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel&lt;/p&gt;&lt;p&gt;Maxim Rubin-Blum&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;School of Environmental Sciences, University of East Anglia, Norwich, UK&lt;/p&gt;&lt;p&gt;Colin Murrell&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel&lt;/p&gt;&lt;p&gt;Werner Eckert&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;Quadram Institute Bioscience, Norwich Research Park, Norwich, UK&lt;/p&gt;&lt;p&gt;Nasmille Larke-Mejía&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel&lt;/p&gt;&lt;p&gt;Maxim Rubin-Blum&lt;/p&gt;&lt;/li&gt;&lt;/ol&gt;&lt;span&gt;Authors&lt;/span&gt;&lt;ol&gt;&lt;li&gt;&lt;span&gt;Almog Gafni&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Maxim Rubin-Blum&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Colin Murrell&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Hanni Vigderovich&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Werner Eckert&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Nasmille Larke-Mejía&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Orit Sivan&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;/ol&gt;&lt;h3&gt;Corresponding author&lt;/h3&gt;&lt;p&gt;Correspondence to Almog Gafni.&lt;/p&gt;&lt;h3&gt;Publisher's Note&lt;/h3&gt;&lt;p&gt;Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.&lt;/p&gt;&lt;p&gt;Article corrected in 2024.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Open Access&lt;/b&gt; 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}