Environmental Microbiology Reports最新文献

{"title":"The impacts of water quality on the amphibian chytrid fungal pathogen: A systematic review","authors":"Adeline Chew,&nbsp;Matt West,&nbsp;Lee Berger,&nbsp;Laura A. Brannelly","doi":"10.1111/1758-2229.13274","DOIUrl":"10.1111/1758-2229.13274","url":null,"abstract":"<p>The pathogenic fungus <i>Batrachochytrium dendrobatidis</i> has caused declines of amphibians worldwide. Yet our understanding of how water quality influences fungal pathogenicity is limited. Here, we reviewed experimental studies on the effect of water quality on this pathogen to determine which parameters impacted disease dynamics consistently. The strongest evidence for protective effects is salinity which shows strong antifungal properties in hosts at natural levels. Although many fungicides had detrimental effects on the fungal pathogen in vitro, their impact on the host is variable and they can worsen infection outcomes. However, one fungicide, epoxiconazole, reduced disease effects experimentally and likely in the field. While heavy metals are frequently studied, there is weak evidence that they influence infection outcomes. Nitrogen and phosphorous do not appear to impact pathogen growth or infection in the amphibian host. The effects of other chemicals, like pesticides and disinfectants on infection were mostly unclear with mixed results or lacking an in vivo component. Our study shows that water chemistry does impact disease dynamics, but the effects of specific parameters require more investigation. Improving our understanding of how water chemistry influences disease dynamics will help predict the impact of chytridiomycosis, especially in amphibian populations affected by land use changes.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"16 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13274","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141074861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-selective microbiota reduction after the elicitation of a seaweed's immune response","authors":"Jiasui Li,&nbsp;Mahasweta Saha,&nbsp;Marwan E. Majzoub,&nbsp;Teng Yang,&nbsp;Haiyan Chu,&nbsp;Torsten Thomas,&nbsp;Florian Weinberger,&nbsp;Suhelen Egan","doi":"10.1111/1758-2229.13268","DOIUrl":"10.1111/1758-2229.13268","url":null,"abstract":"<p>Pattern-triggered immunity (PTI) is an integral part of the innate immune system of many eukaryotic hosts, assisting in the defence against pathogen invasions. In plants and animals, PTI exerts a selective pressure on the microbiota that can alter community composition. However, the effect of PTI on the microbiota for non-model hosts, including seaweeds, remains unknown. Using quantitative polymerase chain reaction complemented with 16S rRNA gene and transcript amplicon sequencing, this study profiled the impact that PTI of the red seaweed <i>Gracilaria gracilis</i> has on its microbiota. PTI elicitation with agar oligosaccharides resulted in a significant reduction in the number of bacteria (by &gt;75% within 72 h after treatment). However, the PTI elicitation did not cause any significant difference in the community diversity or structure. These findings demonstrated that PTI can be non-selective, and this might help to maintain a stable microbiota by uniformly reducing bacterial loads.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"16 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11101764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140955070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dust sprinkling as an effective method for infecting layer chickens with wild-type Salmonella Typhimurium and changes in host gut microbiota","authors":"Samiullah Khan,&nbsp;Andrea R. McWhorter,&nbsp;Daniel M. Andrews,&nbsp;Gregory J. Underwood,&nbsp;Robert J. Moore,&nbsp;Thi Thu Hao Van,&nbsp;Richard K. Gast,&nbsp;Kapil K. Chousalkar","doi":"10.1111/1758-2229.13265","DOIUrl":"10.1111/1758-2229.13265","url":null,"abstract":"<p>Role of dust in <i>Salmonella</i> transmission on chicken farms is not well characterised. <i>Salmonella</i> Typhimurium (ST) infection of commercial layer chickens was investigated using a novel sprinkling method of chicken dust spiked with ST and the uptake compared to a conventional oral infection. While both inoculation methods resulted in colonisation of the intestines, the <i>Salmonella</i> load in liver samples was significantly higher at 7 dpi after exposing chicks to sprinkled dust compared to the oral infection group. Infection of chickens using the sprinkling method at a range of doses showed a threshold for colonisation of the gut and organs as low as 1000 CFU/g of dust. Caecal content microbiota analysis post-challenge showed that the profiles of chickens infected by the sprinkling and oral routes were not significantly different; however, both challenges induced differences when compared to the uninfected negative controls. Overall, the study showed that dust sprinkling was an effective way to experimentally colonise chickens with <i>Salmonella</i> and alter the gut microbiota than oral gavage at levels as low as 1000 CFU/g dust. This infection model mimics the field scenario of <i>Salmonella</i> infection in poultry sheds. The model can be used for future challenge studies for effective <i>Salmonella</i> control.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"16 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13265","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140920739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Zoonotic bacterial and parasitic intestinal pathogens in foxes, raccoons and other predators from eastern Germany","authors":"Sonja Kittl,&nbsp;Caroline F. Frey,&nbsp;Isabelle Brodard,&nbsp;Nadia Scalisi,&nbsp;Maria Elena Vargas Amado,&nbsp;Andreas Thomann,&nbsp;Peter Schierack,&nbsp;Joerg Jores","doi":"10.1111/1758-2229.13261","DOIUrl":"10.1111/1758-2229.13261","url":null,"abstract":"<p>In this study, we investigated faecal specimens from legally hunted and road-killed red foxes, raccoons, raccoon dogs, badgers and martens in Germany for parasites and selected zoonotic bacteria. We found that <i>Baylisascaris procyonis</i>, a zoonotic parasite of raccoons, had spread to northeastern Germany, an area previously presumed to be free of this parasite. We detected various pathogenic bacterial species from the genera <i>Listeria</i>, <i>Clostridium</i> (including <i>baratii</i>), <i>Yersinia</i> and <i>Salmonella</i>, which were analysed using whole-genome sequencing. One isolate of <i>Yersinia enterocolitica</i> contained a virulence plasmid. The <i>Salmonella</i> Cholerasuis isolate encoded an aminoglycoside resistance gene and a <i>parC</i> point mutation, conferring resistance to ciprofloxacin. We also found tetracycline resistance genes in <i>Paeniclostridium sordellii</i> and <i>Clostridium baratii</i>. Phylogenetic analyses revealed that the isolates were polyclonal, indicating the absence of specific wildlife-adapted clones. Predators, which scavenge from various sources including human settlements, acquire and spread zoonotic pathogens. Therefore, their role should not be overlooked in the One Health context.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"16 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13261","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140920742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How do phytophagous insects affect phyllosphere fungi? Tracking fungi from milkweed to monarch caterpillar frass reveals communities dominated by fungal yeast","authors":"Ryoko Oono,&nbsp;Vanessa Chou,&nbsp;Mari Irving","doi":"10.1111/1758-2229.13213","DOIUrl":"10.1111/1758-2229.13213","url":null,"abstract":"<p>Since a significant proportion of plant matter is consumed by herbivores, a necessary adaptation for many phyllosphere microbes could be to survive through the guts of herbivores. While many studies explore the gut microbiome of herbivores by surveying the microbiome in their frass, few studies compare the phyllosphere microbiome to the gut microbiome of herbivores. High-throughput metabarcode sequencing was used to track the fungal community from milkweed (<i>Asclepias</i> spp.) leaves to monarch caterpillar frass. The most commonly identified fungal taxa that dominated the caterpillar frass after the consumption of leaves were yeasts, mostly belonging to the Basidiomycota phylum. While most fungal communities underwent significant bottlenecks and some yeast taxa increased in relative abundance, a consistent directional change in community structure was not identified from leaf to caterpillar frass. These results suggest that some phyllosphere fungi, especially diverse yeasts, can survive herbivory, but whether herbivory is a key stage of their life cycle remains uncertain. For exploring phyllosphere fungi and the potential coprophilous lifestyles of endophytic and epiphytic fungi, methods that target yeast and Basidiomycota fungi are recommended.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"16 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13213","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140910707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic evidence for an energetically advantageous relationship between Syntrophomonas wolfei and Methanothrix soehngenii","authors":"Maaike S. Besteman,&nbsp;Anna Doloman,&nbsp;Diana Z. Sousa","doi":"10.1111/1758-2229.13276","DOIUrl":"https://doi.org/10.1111/1758-2229.13276","url":null,"abstract":"<p>Syntrophic interactions are key in anaerobic food chains, facilitating the conversion of complex organic matter into methane. A typical example involves acetogenic bacteria converting fatty acids (e.g., butyrate and propionate), a process thermodynamically reliant on H₂ consumption by microorganisms such as methanogens. While most studies focus on H₂-interspecies transfer between these groups, knowledge on acetate cross-feeding in anaerobic systems is lacking. This study investigated butyrate oxidation by co-cultures of <i>Syntrophomonas wolfei</i> and <i>Methanospirillum hungatei</i>, both with and without the addition of the acetate scavenger <i>Methanothrix soehngenii</i>. Growth and gene expression patterns of <i>S. wolfei</i> and <i>M. hungatei</i> were followed in the two conditions. Although butyrate consumption rates remained constant, genes in the butyrate degradation pathway of <i>S. wolfei</i> were less expressed in the presence of <i>M. soehngenii</i>, including genes involved in reverse electron transport. Higher expression of a type IV-pili operon in <i>S. wolfei</i> hints to the potential for direct interspecies electron transfer between <i>S. wolfei</i> and <i>M. soehngenii</i> and an energetically advantageous relationship between the two microorganisms. Overall, the presence of the acetate scavenger <i>M. soehngenii</i> positively influenced the energy metabolism of <i>S. wolfei</i> and highlighted the relevance of including acetate scavengers when investigating syntrophic fatty acid degradation.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"16 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13276","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140907040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic evidence for an energetically advantageous relationship between Syntrophomonas wolfei and Methanothrix soehngenii","authors":"Maaike S. Besteman,&nbsp;Anna Doloman,&nbsp;Diana Z. Sousa","doi":"10.1111/1758-2229.13276","DOIUrl":"https://doi.org/10.1111/1758-2229.13276","url":null,"abstract":"<p>Syntrophic interactions are key in anaerobic food chains, facilitating the conversion of complex organic matter into methane. A typical example involves acetogenic bacteria converting fatty acids (e.g., butyrate and propionate), a process thermodynamically reliant on H₂ consumption by microorganisms such as methanogens. While most studies focus on H₂-interspecies transfer between these groups, knowledge on acetate cross-feeding in anaerobic systems is lacking. This study investigated butyrate oxidation by co-cultures of <i>Syntrophomonas wolfei</i> and <i>Methanospirillum hungatei</i>, both with and without the addition of the acetate scavenger <i>Methanothrix soehngenii</i>. Growth and gene expression patterns of <i>S. wolfei</i> and <i>M. hungatei</i> were followed in the two conditions. Although butyrate consumption rates remained constant, genes in the butyrate degradation pathway of <i>S. wolfei</i> were less expressed in the presence of <i>M. soehngenii</i>, including genes involved in reverse electron transport. Higher expression of a type IV-pili operon in <i>S. wolfei</i> hints to the potential for direct interspecies electron transfer between <i>S. wolfei</i> and <i>M. soehngenii</i> and an energetically advantageous relationship between the two microorganisms. Overall, the presence of the acetate scavenger <i>M. soehngenii</i> positively influenced the energy metabolism of <i>S. wolfei</i> and highlighted the relevance of including acetate scavengers when investigating syntrophic fatty acid degradation.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"16 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13276","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140906964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Feeding strategy and feed protein level affect the gut microbiota of common carp (Cyprinus carpio)","authors":"Wouter Mes,&nbsp;Sebastian Lücker,&nbsp;Mike S. M. Jetten,&nbsp;Henk Siepel,&nbsp;Marnix Gorissen,&nbsp;Maartje A. H. J. van Kessel","doi":"10.1111/1758-2229.13262","DOIUrl":"10.1111/1758-2229.13262","url":null,"abstract":"<p>Common carp (<i>Cyprinus carpio</i>) were fed food with different protein concentrations following different feeding regimes, which were previously shown to affect growth, nitrogen excretion and amino acid catabolism. 16S rRNA gene amplicon sequencing was performed to investigate the gut microbiota of these fish. Lower dietary protein content increased microbial richness, while the combination of demand feeding and dietary protein content affected the composition of the gut microbiota. Hepatic glutamate dehydrogenase (GDH) activity was correlated to the composition of the gut microbiota in all dietary treatments. We found that demand-fed carp fed a diet containing 39% protein had a significantly higher abundance of <i>Beijerinckiaceae</i> compared to other dietary groups. Network analysis identified this family and two <i>Rhizobiales</i> families as hubs in the microbial association network. In demand-fed carp, the microbial association network had significantly fewer connections than in batch-fed carp. In contrast to the large effects of the feeding regime and protein content of the food on growth and nitrogen metabolism, it had only limited effects on gut microbiota composition. However, correlations between gut microbiota composition and liver GDH activity showed that host physiology and gut microbiota are connected, which warrants functional studies into the role of the gut microbiota in fish physiology.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"16 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13262","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140896700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The rhizosphere of a drought-tolerant plant species in Morocco: A refuge of high microbial diversity with no taxon preference","authors":"Jean Legeay,&nbsp;Khaoula Errafii,&nbsp;Abdelhadi Ziami,&nbsp;Mohamed Hijri","doi":"10.1111/1758-2229.13254","DOIUrl":"10.1111/1758-2229.13254","url":null,"abstract":"<p>Arid and semi-arid areas are facing increasingly severe water deficits that are being intensified by global climate changes. Microbes associated with plants native to arid regions provide valuable benefits to plants, especially in water-stressed environments. In this study, we used 16S rDNA metabarcoding analysis to examine the bacterial communities in the bulk soil, rhizosphere and root endosphere of the plant <i>Malva sylvestris</i> L. in Morocco, along a gradient of precipitation. We found that the rhizosphere of <i>M. sylvestris</i> did not show significant differences in beta-diversity compared to bulk soil, although, it did display an increased degree of alpha-diversity. The endosphere was largely dominated by the genus <i>Rhizobium</i> and displayed remarkable variation between plants, which could not be attributed to any of the variables observed in this study. Overall, the effects of precipitation level were relatively weak, which may be related to the intense drought in Morocco at the time of sampling. The dominance of <i>Rhizobium</i> in a non-leguminous plant is particularly noteworthy and may permit the utilization of this bacterial taxon to augment drought tolerance; additionally, the absence of any notable selection of the rhizosphere of <i>M. sylvestris</i> suggests that it is not significatively affecting its soil environment.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"16 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13254","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140896701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sulfur cycling likely obscures dynamic biologically-driven iron redox cycling in contemporary methane seep environments","authors":"Isabel R. Baker,&nbsp;Peter R. Girguis","doi":"10.1111/1758-2229.13263","DOIUrl":"https://doi.org/10.1111/1758-2229.13263","url":null,"abstract":"<p>Deep-sea methane seeps are amongst the most biologically productive environments on Earth and are often characterised by stable, low oxygen concentrations and microbial communities that couple the anaerobic oxidation of methane to sulfate reduction or iron reduction in the underlying sediment. At these sites, ferrous iron (Fe²⁺) can be produced by organoclastic iron reduction, methanotrophic-coupled iron reduction, or through the abiotic reduction by sulfide produced by the abundant sulfate-reducing bacteria at these sites. The prevalence of Fe²⁺in the anoxic sediments, as well as the availability of oxygen in the overlying water, suggests that seeps could also harbour communities of iron-oxidising microbes. However, it is unclear to what extent Fe²⁺ remains bioavailable and in solution given that the abiotic reaction between sulfide and ferrous iron is often assumed to scavenge all ferrous iron as insoluble iron sulfides and pyrite. Accordingly, we searched the sea floor at methane seeps along the Cascadia Margin for microaerobic, neutrophilic iron-oxidising bacteria, operating under the reasoning that if iron-oxidising bacteria could be isolated from these environments, it could indicate that porewater Fe²⁺ can persist is long enough for biology to outcompete pyritisation. We found that the presence of sulfate in our enrichment media muted any obvious microbially-driven iron oxidation with most iron being precipitated as iron sulfides. Transfer of enrichment cultures to sulfate-depleted media led to dynamic iron redox cycling relative to abiotic controls and sulfate-containing cultures, and demonstrated the capacity for biogenic iron (oxyhydr)oxides from a methane seep-derived community. 16S rRNA analyses revealed that removing sulfate drastically reduced the diversity of enrichment cultures and caused a general shift from a Gammaproteobacteria-domainated ecosystem to one dominated by <i>Rhodobacteraceae</i> (<i>Alphaproteobacteria</i>). Our data suggest that, in most cases, sulfur cycling may restrict the biological “ferrous wheel” in contemporary environments through a combination of the sulfur-adapted sediment-dwelling ecosystems and the abiotic reactions they influence.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"16 3","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13263","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140844639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}