Girish R Nair, Bhaveni B Kooverjee, Storme de Scally, Don A Cowan, Thulani P Makhalanyane
In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting meltwater run-off and mobilisation of surface nutrients. Yet, the short-term effects of altered nutrient regimes, on the diversity and function of soil microbiota in poly-extreme environments such as Antarctica, remains poorly understood. We studied these effects by simulating such environments via constructing soil microcosms through augmented carbon, nitrogen, and moisture supplements. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatment groups. Other treatments led to shift in relative abundances of these microbial assemblages with random distributional patterns. Only nitrogen treatment appeared to show clear community structural patterns, with increase in abundance of Proteobacteria (Gammaproteobateria) and decrease in Verrucomicrobiota (Chlamydiae, Verrucomicrobiae). Effects of extracellular enzyme activities and soil parameters on changes in microbial taxa also showed significance impacts of nitrogen treatment. Microbial response to nutrient addition was predicted using structural equation modelling which revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms which showed resilience to nutrient increases. Rather than being resistant to change, these microorganisms rapidly responded to augmented nutrient regimes.
{"title":"Changes in nutrient availability substantially alter bacteria and extracellular enzymatic activities in Antarctic soils","authors":"Girish R Nair, Bhaveni B Kooverjee, Storme de Scally, Don A Cowan, Thulani P Makhalanyane","doi":"10.1093/femsec/fiae071","DOIUrl":"https://doi.org/10.1093/femsec/fiae071","url":null,"abstract":"In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting meltwater run-off and mobilisation of surface nutrients. Yet, the short-term effects of altered nutrient regimes, on the diversity and function of soil microbiota in poly-extreme environments such as Antarctica, remains poorly understood. We studied these effects by simulating such environments via constructing soil microcosms through augmented carbon, nitrogen, and moisture supplements. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatment groups. Other treatments led to shift in relative abundances of these microbial assemblages with random distributional patterns. Only nitrogen treatment appeared to show clear community structural patterns, with increase in abundance of Proteobacteria (Gammaproteobateria) and decrease in Verrucomicrobiota (Chlamydiae, Verrucomicrobiae). Effects of extracellular enzyme activities and soil parameters on changes in microbial taxa also showed significance impacts of nitrogen treatment. Microbial response to nutrient addition was predicted using structural equation modelling which revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms which showed resilience to nutrient increases. Rather than being resistant to change, these microorganisms rapidly responded to augmented nutrient regimes.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140840323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Min Shen, Limeng Wu, Yanzhou Zhang, Ruiqiang You, Jiaxin Xiao, Yijun Kang
Cynanchum auriculatum Royle ex Wight (CA) is experiencing challenges with continuous cropping obstacle (CCO) due to soil-borne fungal pathogens. The leaf litter from CA is regularly incorporated into the soil after root harvesting, but the impact of this practice on pathogen outbreaks remains uncertain. In this study, a fungal strain D1, identified as Fusarium solani, was isolated and confirmed as a potential factor in CCO. Both leave extract (LE) and root extract (RE) were found to inhibit seed germination and the activities of plant defense-related enzymes. The combinations of extracts and D1 exacerbated these negative effects. Beyond promoting the proliferation of D1 in soil, the extracts also enhanced the hypha weight, spore number, and spore germination rate of D1. Compared to RE, LE exhibited a greater degree of promotion in the activities of pathogenesis-related enzymes in D1. Additionally, caffeic acid and ferulic acid were identified as potential active compounds. LE, particularly in combination with D1, induced a shift in the composition of fungal communities rather than bacterial communities. These findings indicate that the water extract of leaf litter stimulated the growth and proliferation of fungal strain D1, thereby augmenting its pathogenicity towards CA and ultimately contributing to the CCO process.
由于土壤传播的真菌病原体，Cynanchum auriculatum Royle ex Wight（CA）在连作障碍（CCO）方面遇到了挑战。在根部收获后，CA 的落叶会定期融入土壤，但这种做法对病原体爆发的影响仍不确定。在这项研究中，分离出了一种真菌菌株 D1，经鉴定为 Fusarium solani，并证实它是导致 CCO 的潜在因素。研究发现，叶提取物（LE）和根提取物（RE）都能抑制种子萌发和植物防御相关酶的活性。提取物和 D1 的组合加剧了这些负面影响。除了促进 D1 在土壤中的增殖外，萃取物还提高了 D1 的菌丝重量、孢子数量和孢子萌发率。与 RE 相比，LE 对 D1 的致病相关酶的活性有更大程度的促进作用。此外，咖啡酸和阿魏酸也被确定为潜在的活性化合物。LE，特别是与 D1 结合使用时，诱导真菌群落而不是细菌群落的组成发生变化。这些发现表明，枯落叶水提取物刺激了真菌菌株 D1 的生长和增殖，从而增强了其对 CA 的致病性，并最终促进了 CCO 过程。
{"title":"Leaf litter from Cynanchum auriculatum Royle ex Wight leads to root rot outbreaks by Fusarium solani, hindering continuous cropping","authors":"Min Shen, Limeng Wu, Yanzhou Zhang, Ruiqiang You, Jiaxin Xiao, Yijun Kang","doi":"10.1093/femsec/fiae068","DOIUrl":"https://doi.org/10.1093/femsec/fiae068","url":null,"abstract":"Cynanchum auriculatum Royle ex Wight (CA) is experiencing challenges with continuous cropping obstacle (CCO) due to soil-borne fungal pathogens. The leaf litter from CA is regularly incorporated into the soil after root harvesting, but the impact of this practice on pathogen outbreaks remains uncertain. In this study, a fungal strain D1, identified as Fusarium solani, was isolated and confirmed as a potential factor in CCO. Both leave extract (LE) and root extract (RE) were found to inhibit seed germination and the activities of plant defense-related enzymes. The combinations of extracts and D1 exacerbated these negative effects. Beyond promoting the proliferation of D1 in soil, the extracts also enhanced the hypha weight, spore number, and spore germination rate of D1. Compared to RE, LE exhibited a greater degree of promotion in the activities of pathogenesis-related enzymes in D1. Additionally, caffeic acid and ferulic acid were identified as potential active compounds. LE, particularly in combination with D1, induced a shift in the composition of fungal communities rather than bacterial communities. These findings indicate that the water extract of leaf litter stimulated the growth and proliferation of fungal strain D1, thereby augmenting its pathogenicity towards CA and ultimately contributing to the CCO process.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140840145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yossi Cohen, Julia Johnke, Alfred Abed-Rabbo, Zohar Pasternak, Antonis Chatzinotas, Edouard Jurkevitch
Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics, and functions of the microbial communities in highly sewage-impacted rivers is limited in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem we show, using 16S and 18S rRNA gene-based community analysis and targeted QPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Organic compounds hydrolyzers, and nitrogen and phosphorus recyclers were lacking, pointing at a reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio-and-like-organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.
{"title":"Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream","authors":"Yossi Cohen, Julia Johnke, Alfred Abed-Rabbo, Zohar Pasternak, Antonis Chatzinotas, Edouard Jurkevitch","doi":"10.1093/femsec/fiae069","DOIUrl":"https://doi.org/10.1093/femsec/fiae069","url":null,"abstract":"Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics, and functions of the microbial communities in highly sewage-impacted rivers is limited in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem we show, using 16S and 18S rRNA gene-based community analysis and targeted QPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Organic compounds hydrolyzers, and nitrogen and phosphorus recyclers were lacking, pointing at a reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio-and-like-organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140840325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Masaru Bamba, Turgut Yigit Akyol, Yusuke Azuma, Johan Quilbe, Stig Uggerhøj Andersen, Shusei Sato
The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype [G], soil microbiome [M], and growth conditions (environment) [E] are the core factors shaping root microbiome, their relationships remain unclear. In this study we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.
植物及其根系微生物组之间的生物相互作用对植物生长至关重要，尽管植物基因型[G]、土壤微生物组[M]和生长条件（环境）[E]是影响根系微生物组的核心因素，但它们之间的关系仍不清楚。在本研究中，我们采用体外交叉接种方法，重建了两种不同环境条件下 9 个莲花品种与 4 种土壤微生物组之间的相互作用，研究了 G、M 和 E 及其相互作用对莲花根系微生物组和植物生长的影响。结果表明，根部微生物组的大部分组成是由 M 和 E 决定的，而与 G 相关的（G、G × M 和 G × E）效应显著但较小。相比之下，G 和 M 之间的相互作用对植物嫩枝生长的影响比单独 M 的影响更明显。我们的研究结果还表明，大多数由 M 控制的微生物组变异对植物表型的影响很小，而 G × M 的相互作用则有更显著的影响。植物基因型与土壤微生物之间的相互作用值得更多关注，以优化作物产量和抗逆性。
{"title":"Synergistic effects of plant genotype and soil microbiome on growth in Lotus japonicus","authors":"Masaru Bamba, Turgut Yigit Akyol, Yusuke Azuma, Johan Quilbe, Stig Uggerhøj Andersen, Shusei Sato","doi":"10.1093/femsec/fiae056","DOIUrl":"https://doi.org/10.1093/femsec/fiae056","url":null,"abstract":"The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype [G], soil microbiome [M], and growth conditions (environment) [E] are the core factors shaping root microbiome, their relationships remain unclear. In this study we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140812421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups—bacterial viruses, i.e. phages—has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
{"title":"The role of rhizosphere phages in soil health","authors":"Xiaofang Wang, Yike Tang, Xiufeng Yue, Shuo Wang, Keming Yang, Yangchun Xu, Qirong Shen, Ville-Petri Friman, Zhong Wei","doi":"10.1093/femsec/fiae052","DOIUrl":"https://doi.org/10.1093/femsec/fiae052","url":null,"abstract":"While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups—bacterial viruses, i.e. phages—has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140812940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Deirdre Mikkelsen, Alexandra M. McGowan, Justine S Gibson, J. Lanyon, Sara Horsman, Jennifer M Seddon
Gut bacterial communities play a vital role in a host's digestion, fermentation of complex carbohydrates, absorption of nutrients and energy harvest/storage. Dugongs are obligate seagrass grazers with an expanded hindgut and associated microbiome. Here, we characterised and compared the faecal bacterial communities of dugongs from genetically distinct populations along the east coast of Australia, between subtropical Moreton Bay and tropical Cleveland Bay. Amplicon sequencing of fresh dugong faecal samples (n=47) revealed Firmicutes (62%) dominating the faecal bacterial communities across all populations. Several bacterial genera (Bacteroides, Clostridium sensu stricto 1, Blautia and Polaribacter) were detected in samples from all locations, suggesting their importance in seagrass digestion. Principal coordinate analysis showed the three southern-most dugong populations having different faecal bacterial community compositions from northern populations. The relative abundances of the genera Clostridium sensu stricto 13 and dgA-11 gut group were higher, but Bacteroides was lower, in the southern dugong populations, compared to the northern populations, suggesting potential adaptive changes associated with location. This study contributes to our knowledge of the faecal bacterial communities of dugongs inhabiting Australian coastal waters. Future studies of diet selection in relation to seagrass availability throughout the dugong's range will help to advance our understanding of the roles that seagrass species may play in affecting the dugong's faecal bacterial community composition.
肠道细菌群落在宿主的消化、复杂碳水化合物的发酵、营养吸收和能量收获/储存方面发挥着至关重要的作用。儒艮是一种强制性的海草食草动物，其后肠和相关的微生物群都很发达。在这里，我们对澳大利亚东海岸亚热带莫尔顿湾和热带克利夫兰湾之间不同基因种群的儒艮粪便细菌群落进行了描述和比较。新鲜儒艮粪便样本（样本数=47）的扩增子测序显示，在所有种群的粪便细菌群落中，固着菌（62%）占主导地位。在所有地点的样本中都检测到了几个细菌属（Bacteroides、Clostridium sensu stricto 1、Blautia 和 Polaribacter），表明它们在海草消化中的重要性。主坐标分析表明，最南端的三个儒艮种群的粪便细菌群落组成与北部种群不同。与北部种群相比，南部儒艮种群中严格意义上的梭状芽孢杆菌属 13 和 dgA-11 肠道群的相对丰度较高，而乳杆菌属则较低，这表明儒艮的适应性可能与地点有关。这项研究有助于我们了解栖息在澳大利亚沿海水域的儒艮粪便细菌群落。未来对儒艮整个分布区内与海草可用性有关的饮食选择的研究，将有助于加深我们对海草物种在影响儒艮粪便细菌群落组成方面可能发挥的作用的理解。
{"title":"Faecal bacterial communities differ amongst discrete foraging populations of dugongs along the east Australian coast.","authors":"Deirdre Mikkelsen, Alexandra M. McGowan, Justine S Gibson, J. Lanyon, Sara Horsman, Jennifer M Seddon","doi":"10.1093/femsec/fiae051","DOIUrl":"https://doi.org/10.1093/femsec/fiae051","url":null,"abstract":"Gut bacterial communities play a vital role in a host's digestion, fermentation of complex carbohydrates, absorption of nutrients and energy harvest/storage. Dugongs are obligate seagrass grazers with an expanded hindgut and associated microbiome. Here, we characterised and compared the faecal bacterial communities of dugongs from genetically distinct populations along the east coast of Australia, between subtropical Moreton Bay and tropical Cleveland Bay. Amplicon sequencing of fresh dugong faecal samples (n=47) revealed Firmicutes (62%) dominating the faecal bacterial communities across all populations. Several bacterial genera (Bacteroides, Clostridium sensu stricto 1, Blautia and Polaribacter) were detected in samples from all locations, suggesting their importance in seagrass digestion. Principal coordinate analysis showed the three southern-most dugong populations having different faecal bacterial community compositions from northern populations. The relative abundances of the genera Clostridium sensu stricto 13 and dgA-11 gut group were higher, but Bacteroides was lower, in the southern dugong populations, compared to the northern populations, suggesting potential adaptive changes associated with location. This study contributes to our knowledge of the faecal bacterial communities of dugongs inhabiting Australian coastal waters. Future studies of diet selection in relation to seagrass availability throughout the dugong's range will help to advance our understanding of the roles that seagrass species may play in affecting the dugong's faecal bacterial community composition.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140662416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Ranchou-Peyruse, Marion Guignard, P. Chiquet, Guilhem Caumette, Pierre Cézac, Anthony Ranchou-Peyruse
The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of UGS sites, such as deep aquifers, used for natural gas storage into future underground hydrogen storage (UHS) sites is the favored scenario. However, these sites contain microorganisms capable of consuming H2, mainly sulfate reducers and methanogens. Methanogenesis is therefore expected but its intensity must be evaluated. Here, in a deep aquifer used for UGS, 17 sites were sampled, with low sulfate concentrations ranging from 21.9 to 197.8 µM and a slow renewal of formation water. H2 selected communities mainly were composed of the families Methanobacteriaceae and Methanothermobacteriaceae and the genera Desulfovibrio, Thermodesulfovibrio and Desulforamulus. Experiments were done under different conditions, and sulfate reduction, as well as methanogenesis, were demonstrated in the presence of a H2 or H2/CO2 (80/20) gas phase, with or without calcite/site rock. These metabolisms led to an increase in pH up to 10.2 under certain conditions (without CO2). The results suggest competition for CO2 between lithoautotrophs and carbonate mineral precipitation, which could limit microbial H2 consumption.
{"title":"Assessment of the in situ biomethanation potential of a deep aquifer used for natural gas storage.","authors":"M. Ranchou-Peyruse, Marion Guignard, P. Chiquet, Guilhem Caumette, Pierre Cézac, Anthony Ranchou-Peyruse","doi":"10.1093/femsec/fiae066","DOIUrl":"https://doi.org/10.1093/femsec/fiae066","url":null,"abstract":"The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of UGS sites, such as deep aquifers, used for natural gas storage into future underground hydrogen storage (UHS) sites is the favored scenario. However, these sites contain microorganisms capable of consuming H2, mainly sulfate reducers and methanogens. Methanogenesis is therefore expected but its intensity must be evaluated. Here, in a deep aquifer used for UGS, 17 sites were sampled, with low sulfate concentrations ranging from 21.9 to 197.8 µM and a slow renewal of formation water. H2 selected communities mainly were composed of the families Methanobacteriaceae and Methanothermobacteriaceae and the genera Desulfovibrio, Thermodesulfovibrio and Desulforamulus. Experiments were done under different conditions, and sulfate reduction, as well as methanogenesis, were demonstrated in the presence of a H2 or H2/CO2 (80/20) gas phase, with or without calcite/site rock. These metabolisms led to an increase in pH up to 10.2 under certain conditions (without CO2). The results suggest competition for CO2 between lithoautotrophs and carbonate mineral precipitation, which could limit microbial H2 consumption.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140660115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Since their radiation in the Middle Triassic period ∼ 240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.
{"title":"Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont.","authors":"Amanda Williams","doi":"10.1093/femsec/fiae058","DOIUrl":"https://doi.org/10.1093/femsec/fiae058","url":null,"abstract":"Since their radiation in the Middle Triassic period ∼ 240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140672107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
P. M. Hooper, D. Bass, E. J. Feil, W. F. Vincent, C. Lovejoy, C. J. Owen, S. Tsola, A. Jungblut
Cyanobacterial mats are commonly reported as hotspots of microbial diversity across polar environments. These thick, multi-layered microbial communities provide a refuge from extreme environmental conditions, with many species able to grow and coexist despite the low allochthonous nutrient inputs. The visibly dominant phototrophic biomass is dependent on internal nutrient recycling by heterotrophic organisms within the mats, however the specific contribution of heterotrophic protists remains little explored. In this study, mat community diversity was examined along a latitudinal gradient (55-83°N), spanning subarctic taiga, tundra, polar desert, and the High Arctic ice shelves. The prokaryotic and eukaryotic communities were targeted respectively by V4 16S and V9 18S rRNA gene amplicon high-throughput sequencing. Prokaryotic and eukaryotic richness decreased, in tandem with decreasing temperatures and shorter seasons of light availability, from the subarctic to the High Arctic. Taxonomy-based annotation of the protist community revealed diverse phototrophic, mixotrophic and heterotrophic genera in all mat communities, with fewer parasitic taxa in High Arctic communities. Co-occurrence network analysis identified greater heterogeneity in eukaryotic than prokaryotic community structure among cyanobacterial mats across the Canadian Arctic. Our findings highlight the sensitivity of microbial eukaryotes to environmental gradients across northern high latitudes.
{"title":"Arctic cyanobacterial mat community diversity decreases with latitude across the Canadian Arctic.","authors":"P. M. Hooper, D. Bass, E. J. Feil, W. F. Vincent, C. Lovejoy, C. J. Owen, S. Tsola, A. Jungblut","doi":"10.1093/femsec/fiae067","DOIUrl":"https://doi.org/10.1093/femsec/fiae067","url":null,"abstract":"Cyanobacterial mats are commonly reported as hotspots of microbial diversity across polar environments. These thick, multi-layered microbial communities provide a refuge from extreme environmental conditions, with many species able to grow and coexist despite the low allochthonous nutrient inputs. The visibly dominant phototrophic biomass is dependent on internal nutrient recycling by heterotrophic organisms within the mats, however the specific contribution of heterotrophic protists remains little explored. In this study, mat community diversity was examined along a latitudinal gradient (55-83°N), spanning subarctic taiga, tundra, polar desert, and the High Arctic ice shelves. The prokaryotic and eukaryotic communities were targeted respectively by V4 16S and V9 18S rRNA gene amplicon high-throughput sequencing. Prokaryotic and eukaryotic richness decreased, in tandem with decreasing temperatures and shorter seasons of light availability, from the subarctic to the High Arctic. Taxonomy-based annotation of the protist community revealed diverse phototrophic, mixotrophic and heterotrophic genera in all mat communities, with fewer parasitic taxa in High Arctic communities. Co-occurrence network analysis identified greater heterogeneity in eukaryotic than prokaryotic community structure among cyanobacterial mats across the Canadian Arctic. Our findings highlight the sensitivity of microbial eukaryotes to environmental gradients across northern high latitudes.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140668330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gurpreet S Kharey, V. Palace, L. Whyte, Charles W. Greer
The overall impact of a crude oil spill into a pristine freshwater environment in Canada is largely unknown. To evaluate the impact on the native microbial community, a large-scale in situ model experimental spill was conducted to assess the potential role of the natural community to attenuate hydrocarbons. A small volume of conventional heavy crude oil (CHV) was introduced within contained mesocosm enclosures deployed on the shoreline of a freshwater lake. The oil was left to interact with the shoreline for 72 h and then free-floating oil was recovered using common oil spill response methods (i.e. freshwater flushing and capture on oleophilic absorptive media). Residual PAH concentrations returned to near pre-oiling concentrations within 2 months, while the microbial community composition across the water, soil, and sediment matrices of the enclosed oligotrophic freshwater ecosystems did not shift significantly over this period. Metagenomic analysis revealed key polycyclic aromatic and alkane degradation mechanisms also did not change in their relative abundance over the monitoring period. These trends suggest that for small spills (<2 L of oil per 15 m2 of surface freshwater), physical oil recovery reduces PAH concentrations to levels tolerated by the native microbial community. Additionally, the native microbial community present in the monitored pristine freshwater ecosystem possesses the appropriate hydrocarbon degradation mechanisms without prior challenge by hydrocarbon substrates. This study corroborated trends found previously (Kharey et al. 2024) toward freshwater hydrocarbon degradation in an environmentally relevant scale and conditions on the tolerance of residual hydrocarbons in situ.
{"title":"Influence of heavy Canadian crude oil on pristine freshwater boreal lake ecosystems in an experimental oil spill.","authors":"Gurpreet S Kharey, V. Palace, L. Whyte, Charles W. Greer","doi":"10.1093/femsec/fiae054","DOIUrl":"https://doi.org/10.1093/femsec/fiae054","url":null,"abstract":"The overall impact of a crude oil spill into a pristine freshwater environment in Canada is largely unknown. To evaluate the impact on the native microbial community, a large-scale in situ model experimental spill was conducted to assess the potential role of the natural community to attenuate hydrocarbons. A small volume of conventional heavy crude oil (CHV) was introduced within contained mesocosm enclosures deployed on the shoreline of a freshwater lake. The oil was left to interact with the shoreline for 72 h and then free-floating oil was recovered using common oil spill response methods (i.e. freshwater flushing and capture on oleophilic absorptive media). Residual PAH concentrations returned to near pre-oiling concentrations within 2 months, while the microbial community composition across the water, soil, and sediment matrices of the enclosed oligotrophic freshwater ecosystems did not shift significantly over this period. Metagenomic analysis revealed key polycyclic aromatic and alkane degradation mechanisms also did not change in their relative abundance over the monitoring period. These trends suggest that for small spills (<2 L of oil per 15 m2 of surface freshwater), physical oil recovery reduces PAH concentrations to levels tolerated by the native microbial community. Additionally, the native microbial community present in the monitored pristine freshwater ecosystem possesses the appropriate hydrocarbon degradation mechanisms without prior challenge by hydrocarbon substrates. This study corroborated trends found previously (Kharey et al. 2024) toward freshwater hydrocarbon degradation in an environmentally relevant scale and conditions on the tolerance of residual hydrocarbons in situ.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140672949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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