Environmental microbiology最新文献_第9页

Experimental evidence of d-glutamate racemase activity in the uncultivated bacterium Candidatus Saccharimonas aalborgensis 实验证明未培养的奥尔堡酵母菌具有 d-谷氨酸消旋酶活性

IF 5.1 2区生物学

Environmental microbiology Pub Date : 2024-04-01 DOI: 10.1111/1462-2920.16621

Marcos Peñalver, Alberto Paradela, César Palacios-Cuéllar, M. Graciela Pucciarelli, Francisco García-del Portillo

{"title":"Experimental evidence of d-glutamate racemase activity in the uncultivated bacterium Candidatus Saccharimonas aalborgensis","authors":"Marcos Peñalver, Alberto Paradela, César Palacios-Cuéllar, M. Graciela Pucciarelli, Francisco García-del Portillo","doi":"10.1111/1462-2920.16621","DOIUrl":"https://doi.org/10.1111/1462-2920.16621","url":null,"abstract":"The Candidate Phyla Radiation (CPR) encompasses widespread uncultivated bacteria with reduced genomes and limited metabolic capacities. Most CPR bacteria lack the minimal set of enzymes required for peptidoglycan (PG) synthesis, leaving it unclear how these bacteria produce this essential envelope component. In this study, we analysed the distribution of d-amino acid racemases that produce the universal PG components d-glutamate (d-Glu) or d-alanine (d-Ala). We also examined moonlighting enzymes that synthesize d-Glu or d-Ala. Unlike other phyla in the domain Bacteria, CPR bacteria do not exhibit these moonlighting activities and have, at most, one gene encoding either a Glu or Ala racemase. One of these ‘orphan’ racemases is a predicted Glu racemase (MurICPR) from the CPR bacterium Candidatus Saccharimonas aalborgenesis. The expression of MurICPR restores the growth of a Salmonella d-Glu auxotroph lacking its endogenous racemase and results in the substitution of l-Ala by serine as the first residue in a fraction of the PG stem peptides. In vitro, MurICPR exclusively racemizes Glu as a substrate. Therefore, Ca. Saccharimonas aalborgensis may couple Glu racemization to serine and d-Glu incorporation into the stem peptide. Our findings provide the first insights into the synthesis of PG by an uncultivated environmental bacterium and illustrate how to experimentally test enzymatic activities from CPR bacteria related to PG metabolism.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16621","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140333285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats 北极高纬度冰川独特的风化壳生境由离散的微生物微生境组成

IF 5.1 2区生物学

Environmental microbiology Pub Date : 2024-04-01 DOI: 10.1111/1462-2920.16617

Sara M. E. Rassner, Joseph M. Cook, Andrew C. Mitchell, Ian T. Stevens, Tristram D. L. Irvine-Fynn, Andrew J. Hodson, Arwyn Edwards

{"title":"The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats","authors":"Sara M. E. Rassner, Joseph M. Cook, Andrew C. Mitchell, Ian T. Stevens, Tristram D. L. Irvine-Fynn, Andrew J. Hodson, Arwyn Edwards","doi":"10.1111/1462-2920.16617","DOIUrl":"https://doi.org/10.1111/1462-2920.16617","url":null,"abstract":"Sunlight penetrates the ice surfaces of glaciers and ice sheets, forming a water-bearing porous ice matrix known as the weathering crust. This crust is home to a significant microbial community. Despite the potential implications of microbial processes in the weathering crust for glacial melting, biogeochemical cycles, and downstream ecosystems, there have been few explorations of its microbial communities. In our study, we used 16S rRNA gene sequencing and shotgun metagenomics of a Svalbard glacier surface catchment to characterise the microbial communities within the weathering crust, their origins and destinies, and the functional potential of the weathering crust metagenome. Our findings reveal that the bacterial community in the weathering crust is distinct from those in upstream and downstream habitats. However, it comprises two separate micro-habitats, each with different taxa and functional categories. The interstitial porewater is dominated by Polaromonas, influenced by the transfer of snowmelt, and exported via meltwater channels. In contrast, the ice matrix is dominated by Hymenobacter, and its metagenome exhibits a diverse range of functional adaptations. Given that the global weathering crust area and the subsequent release of microbes from it are strongly responsive to climate projections for the rest of the century, our results underscore the pressing need to integrate the microbiome of the weathering crust with other communities and processes in glacial ecosystems.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16617","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140333287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Wolbachia infection negatively impacts Drosophila simulans heat tolerance in a strain- and trait-specific manner 沃尔巴克氏体感染以品系和性状特异性的方式对果蝇的耐热性产生负面影响

IF 5.1 2区生物学

Environmental microbiology Pub Date : 2024-04-01 DOI: 10.1111/1462-2920.16609

Liam F. Ferguson, Perran A. Ross, Belinda van Heerwaarden

{"title":"Wolbachia infection negatively impacts Drosophila simulans heat tolerance in a strain- and trait-specific manner","authors":"Liam F. Ferguson, Perran A. Ross, Belinda van Heerwaarden","doi":"10.1111/1462-2920.16609","DOIUrl":"https://doi.org/10.1111/1462-2920.16609","url":null,"abstract":"The susceptibility of insects to rising temperatures has largely been measured by their ability to survive thermal extremes. However, the capacity for maternally inherited endosymbionts to influence insect heat tolerance has been overlooked. Further, while some studies have addressed the impact of heat on traits like fertility, which can decline at temperatures below lethal thermal limits, none have considered the impact of endosymbionts. Here, we assess the impact of three Wolbachia strains (wRi, wAu and wNo) on the survival and fertility of Drosophila simulans exposed to heat stress during development or as adults. The effect of Wolbachia infection on heat tolerance was generally small and trait/strain specific. Only the wNo infection significantly reduced the survival of adult males after a heat shock. When exposed to fluctuating heat stress during development, the wRi and wAu strains reduced egg-to-adult survival but only the wNo infection reduced male fertility. Wolbachia densities of all three strains decreased under developmental heat stress, but reductions occurred at temperatures above those that reduced host fertility. These findings emphasize the necessity to account for endosymbionts and their effect on both survival and fertility when investigating insect responses to heat stress.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140333288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbial hitchhikers on microplastics: The exchange of aquatic microbes across distinct aquatic habitats 微塑料上的微生物搭便车：水生微生物在不同水生栖息地之间的交换。

IF 5.1 2区生物学

Environmental microbiology Pub Date : 2024-04-01 DOI: 10.1111/1462-2920.16618

Máté Vass, Kesava Priyan Ramasamy, Agneta Andersson

{"title":"Microbial hitchhikers on microplastics: The exchange of aquatic microbes across distinct aquatic habitats","authors":"Máté Vass, Kesava Priyan Ramasamy, Agneta Andersson","doi":"10.1111/1462-2920.16618","DOIUrl":"10.1111/1462-2920.16618","url":null,"abstract":"Microplastics (MPs) have the potential to modify aquatic microbial communities and distribute microorganisms, including pathogens. This poses a potential risk to aquatic life and human health. Despite this, the fate of ‘hitchhiking’ microbes on MPs that traverse different aquatic habitats remains largely unknown. To address this, we conducted a 50-day microcosm experiment, manipulating estuarine conditions to study the exchange of bacteria and microeukaryotes between river, sea and plastisphere using a long-read metabarcoding approach. Our findings revealed a significant increase in bacteria on the plastisphere, including Pseudomonas, Sphingomonas, Hyphomonas, Brevundimonas, Aquabacterium and Thalassolituus, all of which are known for their pollutant degradation capabilities, specifically polycyclic aromatic hydrocarbons. We also observed a strong association of plastic-degrading fungi (i.e., Cladosporium and Plectosphaerella) and early-diverging fungi (Cryptomycota, also known as Rozellomycota) with the plastisphere. Sea MPs were primarily colonised by fungi (70%), with a small proportion of river-transported microbes (1%–4%). The mere presence of MPs in seawater increased the relative abundance of planktonic fungi from 2% to 25%, suggesting significant exchanges between planktonic and plastisphere communities. Using microbial source tracking, we discovered that MPs only dispersed 3.5% and 5.5% of river bacterial and microeukaryotic communities into the sea, respectively. Hence, although MPs select and facilitate the dispersal of ecologically significant microorganisms, drastic compositional changes across distinct aquatic habitats are unlikely.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16618","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140335188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multiple toxins and a protease contribute to the aphid-killing ability of Pseudomonas fluorescens PpR24 多种毒素和一种蛋白酶增强了荧光假单胞菌 PpR24 杀死蚜虫的能力。

IF 5.1 2区生物学

Environmental microbiology Pub Date : 2024-04-01 DOI: 10.1111/1462-2920.16604

Deepa Paliwal, Mojgan Rabiey, Tim H. Mauchline, Keywan Hassani-Pak, Ralf Nauen, Carol Wagstaff, Simon Andrews, Chris Bass, Robert W. Jackson

{"title":"Multiple toxins and a protease contribute to the aphid-killing ability of Pseudomonas fluorescens PpR24","authors":"Deepa Paliwal, Mojgan Rabiey, Tim H. Mauchline, Keywan Hassani-Pak, Ralf Nauen, Carol Wagstaff, Simon Andrews, Chris Bass, Robert W. Jackson","doi":"10.1111/1462-2920.16604","DOIUrl":"10.1111/1462-2920.16604","url":null,"abstract":"Aphids are globally important pests causing damage to a broad range of crops. Due to insecticide resistance, there is an urgent need to develop alternative control strategies. In our previous work, we found Pseudomonas fluorescens PpR24 can orally infect and kill the insecticide-resistant green-peach aphid (Myzus persicae). However, the genetic basis of the insecticidal capability of PpR24 remains unclear. Genome sequencing of PpR24 confirmed the presence of various insecticidal toxins such as Tc (toxin complexes), Rhs (rearrangement hotspot) elements, and other insect-killing proteases. Upon aphids infection with PpR24, RNA-Seq analysis revealed 193 aphid genes were differentially expressed with down-regulation of 16 detoxification genes. In addition, 1325 PpR24 genes (542 were upregulated and 783 downregulated) were subject to differential expression, including genes responsible for secondary metabolite biosynthesis, the iron-restriction response, oxidative stress resistance, and virulence factors. Single and double deletion of candidate virulence genes encoding a secreted protease (AprX) and four toxin components (two TcA-like; one TcB-like; one TcC-like insecticidal toxins) showed that all five genes contribute significantly to aphid killing, particularly AprX. This comprehensive host–pathogen transcriptomic analysis provides novel insight into the molecular basis of bacteria-mediated aphid mortality and the potential of PpR24 as an effective biocontrol agent.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16604","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140335189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake 视线之外，但并非季节之外：一个大型寡营养湖中的硝化细菌分布和种群动态

IF 5.1 2区生物学

Environmental microbiology Pub Date : 2024-03-22 DOI: 10.1111/1462-2920.16616

Logan M. Peoples, Miranda H. Seixas, Kate A. Evans, Evan M. Bilbrey, John R. Ranieri, Tyler H. Tappenbeck, John E. Dore, Adam Baumann, Matthew J. Church

{"title":"Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake","authors":"Logan M. Peoples, Miranda H. Seixas, Kate A. Evans, Evan M. Bilbrey, John R. Ranieri, Tyler H. Tappenbeck, John E. Dore, Adam Baumann, Matthew J. Church","doi":"10.1111/1462-2920.16616","DOIUrl":"10.1111/1462-2920.16616","url":null,"abstract":"Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia-oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite-oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia-oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16616","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140189103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Host population crashes disrupt the diversity of associated marine microbiomes 宿主群体崩溃破坏了相关海洋微生物群的多样性

IF 5.1 2区生物学

Environmental microbiology Pub Date : 2024-03-22 DOI: 10.1111/1462-2920.16611

William S. Pearman, Sergio E. Morales, Felix Vaux, Neil J. Gemmell, Ceridwen I. Fraser

{"title":"Host population crashes disrupt the diversity of associated marine microbiomes","authors":"William S. Pearman, Sergio E. Morales, Felix Vaux, Neil J. Gemmell, Ceridwen I. Fraser","doi":"10.1111/1462-2920.16611","DOIUrl":"https://doi.org/10.1111/1462-2920.16611","url":null,"abstract":"Host-associated microbial communities are shaped by myriad factors ranging from host conditions, environmental conditions and other microbes. Disentangling the ecological impact of each of these factors can be particularly difficult as many variables are correlated. Here, we leveraged earthquake-induced changes in host population structure to assess the influence of population crashes on marine microbial ecosystems. A large (7.8 magnitude) earthquake in New Zealand in 2016 led to widespread coastal uplift of up to ~6 m, sufficient to locally extirpate some intertidal southern bull kelp populations. These uplifted populations are slowly recovering, but remain at much lower densities than at nearby, less-uplifted sites. By comparing the microbial communities of the hosts from disturbed and relatively undisturbed populations using 16S rRNA gene amplicon sequencing, we observed that disturbed host populations supported higher functional, taxonomic and phylogenetic microbial beta diversity than non-disturbed host populations. Our findings shed light on microbiome ecological assembly processes, particularly highlighting that large-scale disturbances that affect host populations can dramatically influence microbiome structure. We suggest that disturbance-induced changes in host density limit the dispersal opportunities of microbes, with host community connectivity declining with the density of host populations.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16611","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140192132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A single Prochlorococcus ecotype dominates the tropical Bay of Bengal with ultradian growth 一种单一的 Prochlorococcus 生态型主导着热带孟加拉湾的超昼夜生长

IF 5.1 2区生物学

Environmental microbiology Pub Date : 2024-03-22 DOI: 10.1111/1462-2920.16605

Jonathan Grone, Camille Poirier, Kathleen Abbott, Fabian Wittmers, Gualtiero Spiro Jaeger, Amala Mahadevan, Alexandra Z. Worden

{"title":"A single Prochlorococcus ecotype dominates the tropical Bay of Bengal with ultradian growth","authors":"Jonathan Grone, Camille Poirier, Kathleen Abbott, Fabian Wittmers, Gualtiero Spiro Jaeger, Amala Mahadevan, Alexandra Z. Worden","doi":"10.1111/1462-2920.16605","DOIUrl":"10.1111/1462-2920.16605","url":null,"abstract":"The Bay of Bengal (BoB) spans >2.2 million km2 in the northeastern Indian Ocean and is bordered by dense populations that depend upon its resources. Over recent decades, a shift from larger phytoplankton to picoplankton has been reported, yet the abundance, activity, and composition of primary producer communities are not well-characterized. We analysed the BoB regions during the summer monsoon. Prochlorococcus ranged up to 3.14 × 105 cells mL−1 in the surface mixed layer, averaging 1.74 ± 0.46 × 105 in the upper 10 m and consistently higher than Synechococcus and eukaryotic phytoplankton. V1-V2 rRNA gene amplicon analyses showed the High Light II (HLII) ecotype formed 98 ± 1% of Prochlorococcus amplicons in surface waters, comprising six oligotypes, with the dominant oligotype accounting for 65 ± 4% of HLII. Diel sampling of a coherent water mass demonstrated evening onset of cell division and rapid Prochlorococcus growth between 1.5 and 3.1 div day−1, based on cell cycle analysis, as confirmed by abundance-based estimates of 2.1 div day−1. Accumulation of Prochlorococcus produced by ultradian growth was restricted by high loss rates. Alongside prior Arabian Sea and tropical Atlantic rates, our results indicate Prochlorococcus growth rates should be reevaluated with greater attention to latitudinal zones and influences on contributions to global primary production.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16605","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140189118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air 调查覆盆子果实表面和空气中 Cladosporium 的接种动态。

IF 5.1 2区生物学

Environmental microbiology Pub Date : 2024-03-21 DOI: 10.1111/1462-2920.16613

Lauren Helen Farwell, Matevz Papp-Rupar, Greg Deakin, Naresh Magan, Xiangming Xu

{"title":"Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air","authors":"Lauren Helen Farwell, Matevz Papp-Rupar, Greg Deakin, Naresh Magan, Xiangming Xu","doi":"10.1111/1462-2920.16613","DOIUrl":"10.1111/1462-2920.16613","url":null,"abstract":"Raspberry production is under threat from the emerging fungal pathogenic genus Cladosporium. We used amplicon-sequencing, coupled with qPCR, to investigate how fruit age, fruit location within a polytunnel, polytunnel location and sampling date affected the fruit epiphytic microbiome. Fruit age was the most important factor impacting the fungal microbiome, followed by sampling date and polytunnel location. In contrast, polytunnel location and fruit age were important factors impacting the bacterial microbiome composition, followed by the sampling date. The within-tunnel location had a small significant effect on the fungal microbiome and no effect on the bacterial microbiome. As fruit ripened, fungal diversity increased and the bacterial diversity decreased. Cladosporium was the most abundant fungus of the fruit epiphytic microbiome, accounting for nearly 44% of all fungal sequences. Rotorod air samplers were used to study how the concentration of airborne Cladosporium inoculum (quantified by qPCR) varied between location (inside and outside the polytunnel) and time (daytime vs. nighttime). Quantified Cladosporium DNA was significantly higher during the day than the night and inside the polytunnel than the outside. This study demonstrated the dynamic nature of epiphytic raspberry fruit microbiomes and airborne Cladosporium inoculum within polytunnels, which will impact disease risks on raspberry fruit.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16613","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140179474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation 基于 DNA 的全球环境调查在检测所有原生生物多样性方面的效果如何？以 Arcellinida 为例，说明其代表性存在偏差。

IF 5.1 2区生物学

Environmental microbiology Pub Date : 2024-03-20 DOI: 10.1111/1462-2920.16606

Fernando Useros, Iván García-Cunchillos, Nicolas Henry, Cédric Berney, Enrique Lara

{"title":"How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation","authors":"Fernando Useros, Iván García-Cunchillos, Nicolas Henry, Cédric Berney, Enrique Lara","doi":"10.1111/1462-2920.16606","DOIUrl":"10.1111/1462-2920.16606","url":null,"abstract":"Metabarcoding approaches targeting microeukaryotes have deeply changed our vision of protist environmental diversity. The public repository EukBank consists of 18S v4 metabarcodes from 12,672 samples worldwide. To estimate how far this database provides a reasonable overview of all eukaryotic diversity, we used Arcellinida (lobose testate amoebae) as a case study. We hypothesised that (1) this approach would allow the discovery of unexpected diversity, but also that (2) some groups would be underrepresented because of primer/sequencing biases. Most of the Arcellinida sequences appeared in freshwater and soil, but their abundance and diversity appeared underrepresented. Moreover, 84% of ASVs belonged to the suborder Phryganellina, a supposedly species-poor clade, whereas the best-documented suborder (Glutinoconcha, 600 described species) was only marginally represented. We explored some possible causes of these biases. Mismatches in the primer-binding site seem to play a minor role. Excessive length of the target region could explain some of these biases, but not all. There must be some other unknown factors involved. Altogether, while metabarcoding based on ribosomal genes remains a good first approach to document microbial eukaryotic clades, alternative approaches based on other genes or sequencing techniques must be considered for an unbiased picture of the diversity of some groups.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16606","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140179473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0