Environmental Microbiome最新文献

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The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter 巨型碳酸月乳结构的微生物群特征及其与保存的有机物的相关性
IF 7.9 2区 环境科学与生态学
Environmental Microbiome Pub Date : 2024-04-24 DOI: 10.1186/s40793-024-00562-9
Daniele Ghezzi, N. T. Jiménez-Morillo, Lisa Foschi, Eva Donini, V. Chiarini, J. De Waele, Ana Zélia Miller, Martina Cappelletti
{"title":"The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter","authors":"Daniele Ghezzi, N. T. Jiménez-Morillo, Lisa Foschi, Eva Donini, V. Chiarini, J. De Waele, Ana Zélia Miller, Martina Cappelletti","doi":"10.1186/s40793-024-00562-9","DOIUrl":"https://doi.org/10.1186/s40793-024-00562-9","url":null,"abstract":"","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140664246","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}
引用次数: 0
Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact 嫁接葡萄树的接穗和砧木都会影响根圈和根内生微生物群,但砧木的影响更大
IF 7.9 2区 环境科学与生态学
Environmental Microbiome Pub Date : 2024-04-23 DOI: 10.1186/s40793-024-00566-5
Vincent Lailheugue, Romain Darriaut, Joseph Tran, Marine Morel, E. Marguerit, Virginie Lauvergeat
{"title":"Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact","authors":"Vincent Lailheugue, Romain Darriaut, Joseph Tran, Marine Morel, E. Marguerit, Virginie Lauvergeat","doi":"10.1186/s40793-024-00566-5","DOIUrl":"https://doi.org/10.1186/s40793-024-00566-5","url":null,"abstract":"","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140665739","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}
引用次数: 0
Wallace’s line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria 华莱士线构造了海草微生物群,是海洋细菌传播的潜在障碍
IF 7.9 2区 环境科学与生态学
Environmental Microbiome Pub Date : 2024-04-18 DOI: 10.1186/s40793-024-00568-3
Benjamin J. Wainwright, Josh Leon, Ernie Vilela, K. J. E. Hickman, Jensen Caldwell, Behlee Aimone, Porter Bischoff, Marissa Ohran, Magnolia W. Morelli, Irma S. Arlyza, Onny N. Marwayana, Geoffrey Zahn
{"title":"Wallace’s line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria","authors":"Benjamin J. Wainwright, Josh Leon, Ernie Vilela, K. J. E. Hickman, Jensen Caldwell, Behlee Aimone, Porter Bischoff, Marissa Ohran, Magnolia W. Morelli, Irma S. Arlyza, Onny N. Marwayana, Geoffrey Zahn","doi":"10.1186/s40793-024-00568-3","DOIUrl":"https://doi.org/10.1186/s40793-024-00568-3","url":null,"abstract":"The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace’s line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line. We found significant differences in microbial community structure on either side of this boundary (R2 = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community. Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140612932","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}
引用次数: 0
Niche–dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis 取决于生境的海绵全基因组表达谱以及宿主与微生物之间的相互作用:以夏威夷海绵Mycale Grandis为例
IF 7.9 2区 环境科学与生态学
Environmental Microbiome Pub Date : 2024-04-08 DOI: 10.1186/s40793-024-00563-8
Fang Liu, Taewoo Ryu, Timothy Ravasi, Xin Wang, Guangyi Wang, Zhiyong Li
{"title":"Niche–dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis","authors":"Fang Liu, Taewoo Ryu, Timothy Ravasi, Xin Wang, Guangyi Wang, Zhiyong Li","doi":"10.1186/s40793-024-00563-8","DOIUrl":"https://doi.org/10.1186/s40793-024-00563-8","url":null,"abstract":"Most researches on sponge holobionts focus primarily on symbiotic microbes, yet data at the level of the sponge hologenome are still relatively scarce. Understanding of the sponge host and its microbial gene expression profiles and the host-microbes interplay in different niches represents a key aspect of sponge hologenome. Using the Hawaiian demosponge Mycale grandis in different niches as a model, i.e. on rocks, on the surface of coral Porites compressa, under alga Gracilaria salicornia, we compared the bacterial and fungal community structure, functional gene diversity, expression pattern and the host transcriptome by integrating open-format (deep sequencing) and closed-format (GeoChip microarray) high-throughput techniques. Little inter-niche variation in bacterial and fungal phylogenetic diversity was detected for M. grandis in different niches, but a clear niche-dependent variability in the functional gene diversity and expression pattern of M. grandis host and its symbiotic microbiota was uncovered by GeoChip microarray and transcriptome analyses. Particularly, sponge host genes related to innate immunity and microbial recognition showed a strong correlation with the microbial symbionts’ functional gene diversity and transcriptional richness in different niches. The cross-niche variability with respect to the symbiont functional gene diversity and the transcriptional richness of M. grandis holobiont putatively reflects the interplay of niche-specific selective pressure and the symbiont functional diversity. Niche–dependent gene expression profiles of M. grandis hologenome and the host-microbes interplay were suggested though little inter-niche variation in bacterial and fungal diversity was detected, particularly the sponge innate immunity was found to be closely related to the symbiotic microbes. Altogether, these findings provide novel insights into the black box of one sponge holobiont in different niches at the hologenome level.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140575225","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}
引用次数: 0
Forest top canopy bacterial communities are influenced by elevation and host tree traits 森林顶冠细菌群落受海拔高度和寄主树特性的影响
IF 7.9 2区 环境科学与生态学
Environmental Microbiome Pub Date : 2024-04-05 DOI: 10.1186/s40793-024-00565-6
Yiwei Duan, Andjin Siegenthaler, Andrew K. Skidmore, Anthony A. Chariton, Ivo Laros, Mélody Rousseau, G. Arjen De Groot
{"title":"Forest top canopy bacterial communities are influenced by elevation and host tree traits","authors":"Yiwei Duan, Andjin Siegenthaler, Andrew K. Skidmore, Anthony A. Chariton, Ivo Laros, Mélody Rousseau, G. Arjen De Groot","doi":"10.1186/s40793-024-00565-6","DOIUrl":"https://doi.org/10.1186/s40793-024-00565-6","url":null,"abstract":"The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce). We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families. While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140575165","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}
引用次数: 0
Fungal and bacterial communities and their associations in snow-free and snow covered (sub-)alpine Pinus cembra forest soils 无雪和有(亚)雪覆盖的高山 Pinus cembra 森林土壤中的真菌和细菌群落及其联系
IF 7.9 2区 环境科学与生态学
Environmental Microbiome Pub Date : 2024-04-02 DOI: 10.1186/s40793-024-00564-7
Maraike Probst, Anusha Telagathoti, Edoardo Mandolini, Ursula Peintner
{"title":"Fungal and bacterial communities and their associations in snow-free and snow covered (sub-)alpine Pinus cembra forest soils","authors":"Maraike Probst, Anusha Telagathoti, Edoardo Mandolini, Ursula Peintner","doi":"10.1186/s40793-024-00564-7","DOIUrl":"https://doi.org/10.1186/s40793-024-00564-7","url":null,"abstract":"In Europe, Pinus cembra forests cover subalpine and alpine areas and they are of high conservational and ecological relevance. These forests experience strong seasonality with alternating snow-free and snow covered periods. Although P. cembra is known for mycorrhization and mycorrhizae usually involve fungi, plants and bacteria, the community compositions of fungi and bacteria and their associations in (sub-)alpine P. cembra forests remain vastly understudied. Here, we studied the fungal and bacterial community compositions in three independent (sub-)alpine P. cembra forests and inferred their microbial associations using marker gene sequencing and network analysis. We asked about the effect of snow cover on microbial compositions and associations. In addition, we propose inferring microbial associations across a range of filtering criteria, based on which we infer well justified, concrete microbial associations with high potential for ecological relevance that are typical for P. cembra forests and depending on snow cover. The overall fungal and bacterial community structure was comparable with regards to both forest locations and snow cover. However, occurrence, abundance, and diversity patterns of several microbial taxa typical for P. cembra forests differed among snow-free and snow covered soils, e.g. Russula, Tetracladium and Phenoliphera. Moreover, network properties and microbial associations were influenced by snow cover. Here, we present concrete microbial associations on genus and species level that were repeatedly found across microbial networks, thereby confirming their ecological relevance. Most importantly, ectomycorrhizal fungi, such as Basidioascus, Pseudotomentella and Rhizopogon, as well as saprobic Mortierella changed their bacterial association partners depending on snow cover. This is the first study researching fungal-bacterial associations across several (sub-)alpine P. cembra forests. The poorly investigated influence of snow cover on soil fungi and bacteria, especially those mycorrhizing P. cembra roots, but also saprobic soil organisms, underlines the relevance of forest seasonality. Our findings highlight that the seasonal impact of snow cover has significant consequences for the ecology of the ecosystem, particularly in relation to mycorrhization and nutrient cycling. It is imperative to consider such effects for a comprehensive understanding of the functioning resilience and responsiveness of an ecosystem.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140575250","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}
引用次数: 0
An in-depth evaluation of metagenomic classifiers for soil microbiomes. 深入评估用于土壤微生物组的元基因组分类器。
IF 7.9 2区 环境科学与生态学
Environmental Microbiome Pub Date : 2024-03-28 DOI: 10.1186/s40793-024-00561-w
Niranjana Rose Edwin, Amy Heather Fitzpatrick, Fiona Brennan, Florence Abram, Orla O'Sullivan
{"title":"An in-depth evaluation of metagenomic classifiers for soil microbiomes.","authors":"Niranjana Rose Edwin, Amy Heather Fitzpatrick, Fiona Brennan, Florence Abram, Orla O'Sullivan","doi":"10.1186/s40793-024-00561-w","DOIUrl":"10.1186/s40793-024-00561-w","url":null,"abstract":"<p><strong>Background: </strong>Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy.</p><p><strong>Results: </strong>In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database.</p><p><strong>Conclusion: </strong>This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10979606/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140319543","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}
引用次数: 0
Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly 在土壤定殖过程中操纵细胞间的物理距离,揭示了微生物群落组装过程中生物相互作用的重要性
IF 7.9 2区 环境科学与生态学
Environmental Microbiome Pub Date : 2024-03-19 DOI: 10.1186/s40793-024-00559-4
Sana Romdhane, Sarah Huet, Aymé Spor, David Bru, Marie-Christine Breuil, Laurent Philippot
{"title":"Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly","authors":"Sana Romdhane, Sarah Huet, Aymé Spor, David Bru, Marie-Christine Breuil, Laurent Philippot","doi":"10.1186/s40793-024-00559-4","DOIUrl":"https://doi.org/10.1186/s40793-024-00559-4","url":null,"abstract":"Microbial communities are of tremendous importance for ecosystem functioning and yet we know little about the ecological processes driving the assembly of these communities in the environment. Here, we used an unprecedented experimental approach based on the manipulation of physical distance between neighboring cells during soil colonization to determine the role of bacterial interactions in soil community assembly. We hypothesized that experimentally manipulating the physical distance between bacterial cells will modify the interaction strengths leading to differences in microbial community composition, with increasing distance between neighbors favoring poor competitors. We found significant differences in both bacterial community diversity, composition and co-occurrence networks after soil colonization that were related to physical distancing. We show that reducing distances between cells resulted in a loss of bacterial diversity, with at least 41% of the dominant OTUs being significantly affected by physical distancing. Our results suggest that physical distancing may differentially modulate competitiveness between neighboring species depending on the taxa present in the community. The mixing of communities that assembled at high and low cell densities did not reveal any “home field advantage” during coalescence. This confirms that the observed differences in competitiveness were due to biotic rather than abiotic filtering. Our study demonstrates that the competitiveness of bacteria strongly depends on cell density and community membership, therefore highlighting the fundamental role of microbial interactions in the assembly of soil communities.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140165741","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}
引用次数: 0
City-scale monitoring of antibiotic resistance genes by digital PCR and metagenomics. 通过数字 PCR 和元基因组学监测城市规模的抗生素耐药基因。
IF 6.2 2区 环境科学与生态学
Environmental Microbiome Pub Date : 2024-03-15 DOI: 10.1186/s40793-024-00557-6
Lucia Maestre-Carballa, Vicente Navarro-López, Manuel Martinez-Garcia
{"title":"City-scale monitoring of antibiotic resistance genes by digital PCR and metagenomics.","authors":"Lucia Maestre-Carballa, Vicente Navarro-López, Manuel Martinez-Garcia","doi":"10.1186/s40793-024-00557-6","DOIUrl":"10.1186/s40793-024-00557-6","url":null,"abstract":"<p><strong>Background: </strong>Anthropogenic activities significantly contribute to the dissemination of antibiotic resistance genes (ARGs), posing a substantial threat to humankind. The development of methods that allow robust ARG surveillance is a long-standing challenge. Here, we use city-scale monitoring of ARGs by using two of the most promising cutting-edge technologies, digital PCR (dPCR) and metagenomics.</p><p><strong>Methods: </strong>ARG hot-spots were sampled from the urban water and wastewater distribution systems. Metagenomics was used to provide a broad view of ARG relative abundance and richness in the prokaryotic and viral fractions. From the city-core ARGs in all samples, the worldwide dispersed sul2 and tetW conferring resistance to sulfonamide and tetracycline, respectively, were monitored by dPCR and metagenomics.</p><p><strong>Results: </strong>The largest relative overall ARG abundance and richness were detected in the hospital wastewater and the WWTP inlet (up to ≈6,000 ARGs/Gb metagenome) with a large fraction of unclassified resistant bacteria. The abundance of ARGs in DNA and RNA contigs classified as viruses was notably lower, demonstrating a reduction of up to three orders of magnitude compared to contigs associated to prokaryotes. By metagenomics and dPCR, a similar abundance tendency of sul2 and tetW was obtained, with higher abundances in hospital wastewater and WWTP input (≈125-225 ARGs/Gb metagenome). dPCR absolute abundances were between 6,000 and 18,600 copies per ng of sewage DNA (≈10<sup>5-7</sup> copies/mL) and 6.8 copies/mL in seawater near the WWTP discharging point.</p><p><strong>Conclusions: </strong>dPCR was more sensitive and accurate, while metagenomics provided broader coverage of ARG detection. While desirable, a reliable correlation of dPCR absolute abundance units into metagenomic relative abundance units was not obtained here (r<sup>2</sup> < 0.4) suggesting methodological factors that introduce variability. Evolutionary pressure does not significantly select the targeted ARGs in natural aquatic environments.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10943798/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140893","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}
引用次数: 0
Pitting the olive seed microbiome. 橄榄籽微生物群的提取。
IF 7.9 2区 环境科学与生态学
Environmental Microbiome Pub Date : 2024-03-15 DOI: 10.1186/s40793-024-00560-x
Nuria M Wentzien, Antonio J Fernández-González, Antonio Valverde-Corredor, Ana V Lasa, Pablo J Villadas, Wisnu Adi Wicaksono, Tomislav Cernava, Gabriele Berg, Manuel Fernández-López, Jesús Mercado-Blanco
{"title":"Pitting the olive seed microbiome.","authors":"Nuria M Wentzien, Antonio J Fernández-González, Antonio Valverde-Corredor, Ana V Lasa, Pablo J Villadas, Wisnu Adi Wicaksono, Tomislav Cernava, Gabriele Berg, Manuel Fernández-López, Jesús Mercado-Blanco","doi":"10.1186/s40793-024-00560-x","DOIUrl":"10.1186/s40793-024-00560-x","url":null,"abstract":"<p><strong>Background: </strong>The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter. Therefore, we have developed a methodology for obtaining samples from the olive seed's endosphere under sterile conditions.</p><p><strong>Results: </strong>A diverse microbiota was uncovered in olive seeds, the plant genotype being an important factor influencing the structure and composition of the microbial communities. The most abundant bacterial phylum was Actinobacteria, accounting for an average relative abundance of 41%. At genus level, Streptomyces stood out because of its potential influence on community structure. Within the fungal community, Basidiomycota and Ascomycota were the most abundant phyla, including the genera Malassezia, Cladosporium, and Mycosphaerella. The shared microbiome was composed of four bacterial (Stenotrophomonas, Streptomyces, Promicromonospora and Acidipropionibacterium) and three fungal (Malassezia, Cladosporium and Mycosphaerella) genera. Furthermore, a comparison between findings obtained here and earlier results from the root endosphere of the same trees indicated that genera such as Streptomyces and Malassezia were present in both olive compartments.</p><p><strong>Conclusions: </strong>This study provides the first insights into the composition of the olive seed microbiota. The highly abundant fungal genus Malassezia and the bacterial genus Streptomyces reflect a unique signature of the olive seed microbiota. The genotype clearly shaped the composition of the seed's microbial community, although a shared microbiome was found. We identified genera that may translocate from the roots to the seeds, as they were present in both organs of the same trees. These findings set the stage for future research into potential vertical transmission of olive endophytes and the role of specific microbial taxa in seed germination, development, and seedling survival.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10943921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140894","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}
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