Environmental Microbiology Reports最新文献

Microbial Responses to Micronutrient Amendments in Oxygenated and Deoxygenated Waters of the Arabian Sea 阿拉伯海加氧和脱氧水体中微生物对微量营养素变化的反应

IF 3.6 4区生物学

Environmental Microbiology Reports Pub Date : 2025-05-02 DOI: 10.1111/1758-2229.70072

Mandar Bandekar, Rakhee Khandeparker, Kuldeep D. More, Seyieleno C. Seleyi, Mukund Gauthankar, Ujwala Amberkar, Jukka Kekäläinen, Jarkko Akkanen

{"title":"Microbial Responses to Micronutrient Amendments in Oxygenated and Deoxygenated Waters of the Arabian Sea","authors":"Mandar Bandekar, Rakhee Khandeparker, Kuldeep D. More, Seyieleno C. Seleyi, Mukund Gauthankar, Ujwala Amberkar, Jukka Kekäläinen, Jarkko Akkanen","doi":"10.1111/1758-2229.70072","DOIUrl":"https://doi.org/10.1111/1758-2229.70072","url":null,"abstract":"Metalloenzyme cofactors and oxygen conditions are crucial for microbial metabolism, yet their combined effects on microbial ecosystems remain unexplored. This study explores the impact of micronutrient amendments (Zn, Fe, Co and their combinations) on the microbial community composition in oxygenated (73 m) and deoxygenated (200 m) waters of the Arabian Sea. Through controlled microcosm experiment and 16S rRNA amplicon sequencing, we observed that micronutrients significantly alter nutrient concentrations and microbial dynamics. At 73 m, micronutrient treatments reduced nitrate, nitrite and ammonia levels, whereas at 200 m, they increased nitrate and silicate levels. Total bacterial counts (TBCs) were higher in all treatments at both depths, with Fe showing the highest counts. Alpha diversity indicated that Fe-amended flask increased microbial diversity the most at 73 m, while mixed treatments had a pronounced effect at 200 m. Taxonomic analysis revealed significant genus-level variations in both bacteria and archaea. One-way analysis of variance (ANOVA) confirmed micronutrient impacts on nutrients and TBC. Canonical correspondence analysis (CCA) and non-metric multidimensional scaling (NMDS) revealed distinct clustering based on oxygen conditions. These results confirm our hypothesis that micronutrient amendments in varying oxygen levels distinctly alter microbial community composition and nutrient cycling in marine environments.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"17 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.70072","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143896830","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}

引用次数: 0

Microbial Responses to Micronutrient Amendments in Oxygenated and Deoxygenated Waters of the Arabian Sea 阿拉伯海加氧和脱氧水体中微生物对微量营养素变化的反应

IF 3.6 4区生物学

Environmental Microbiology Reports Pub Date : 2025-05-02 DOI: 10.1111/1758-2229.70072

Mandar Bandekar, Rakhee Khandeparker, Kuldeep D. More, Seyieleno C. Seleyi, Mukund Gauthankar, Ujwala Amberkar, Jukka Kekäläinen, Jarkko Akkanen

{"title":"Microbial Responses to Micronutrient Amendments in Oxygenated and Deoxygenated Waters of the Arabian Sea","authors":"Mandar Bandekar, Rakhee Khandeparker, Kuldeep D. More, Seyieleno C. Seleyi, Mukund Gauthankar, Ujwala Amberkar, Jukka Kekäläinen, Jarkko Akkanen","doi":"10.1111/1758-2229.70072","DOIUrl":"https://doi.org/10.1111/1758-2229.70072","url":null,"abstract":"Metalloenzyme cofactors and oxygen conditions are crucial for microbial metabolism, yet their combined effects on microbial ecosystems remain unexplored. This study explores the impact of micronutrient amendments (Zn, Fe, Co and their combinations) on the microbial community composition in oxygenated (73 m) and deoxygenated (200 m) waters of the Arabian Sea. Through controlled microcosm experiment and 16S rRNA amplicon sequencing, we observed that micronutrients significantly alter nutrient concentrations and microbial dynamics. At 73 m, micronutrient treatments reduced nitrate, nitrite and ammonia levels, whereas at 200 m, they increased nitrate and silicate levels. Total bacterial counts (TBCs) were higher in all treatments at both depths, with Fe showing the highest counts. Alpha diversity indicated that Fe-amended flask increased microbial diversity the most at 73 m, while mixed treatments had a pronounced effect at 200 m. Taxonomic analysis revealed significant genus-level variations in both bacteria and archaea. One-way analysis of variance (ANOVA) confirmed micronutrient impacts on nutrients and TBC. Canonical correspondence analysis (CCA) and non-metric multidimensional scaling (NMDS) revealed distinct clustering based on oxygen conditions. These results confirm our hypothesis that micronutrient amendments in varying oxygen levels distinctly alter microbial community composition and nutrient cycling in marine environments.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"17 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.70072","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143896831","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}

引用次数: 0

Halophilic and Non-Halophilic Microbial Communities in Relation to Physico-Chemical Characteristics of Salt Mine Air 与盐矿空气理化特性相关的嗜盐与非嗜盐微生物群落

IF 3.6 4区生物学

Environmental Microbiology Reports Pub Date : 2025-04-30 DOI: 10.1111/1758-2229.70095

Aleksandra Puławska, Jolanta Kalinowska, Michalina Rachubik, Dominika Drzewiecka, Luciana Albuquerque, Conceiçao Egas, Krzysztof Krawczyk, Maciej Manecki, Camille Locht, Magdalena Kowalewicz-Kulbat

{"title":"Halophilic and Non-Halophilic Microbial Communities in Relation to Physico-Chemical Characteristics of Salt Mine Air","authors":"Aleksandra Puławska, Jolanta Kalinowska, Michalina Rachubik, Dominika Drzewiecka, Luciana Albuquerque, Conceiçao Egas, Krzysztof Krawczyk, Maciej Manecki, Camille Locht, Magdalena Kowalewicz-Kulbat","doi":"10.1111/1758-2229.70095","DOIUrl":"https://doi.org/10.1111/1758-2229.70095","url":null,"abstract":"Salt mines are often used for halotherapy against lung and skin diseases. In addition to salt, they also contain various types of microorganisms, which remain poorly characterised. Here, we examined culturable halophilic and non-halophilic microbial populations in relation to the physico-chemical characteristics in the air of four different sites of the Bochnia Salt Mine, a popular halotherapy resort in Southern Poland. At the mine entrance, the temperature was highest (20.8°C) and decreased with increasing distance from the entrance (15.5°C at 2671 m from entrance), while humidity increased from 55.9% to 77.0%, as did the NaCl concentration. At the entrance, non-halophilic microorganisms prevailed, especially fungi that grew at 21°C. Halophiles gradually dominated with distance from the entrance, including halophilic archaea that grew at 28°C or 37°C on medium containing 15%, 20%, or 25% NaCl. Seven halophilic archaeal species were identified by 16S rRNA gene sequencing. The frequency of non-halophiles was inversely related to distance from the entrance, humidity, and presence of ions, while the reverse was seen for halophiles. An exception was the site used for halotherapy, where non-halophilic bacteria dominated. Thus, natural salt mines contain a wide variety of non-halophilic and halophilic microorganisms, including archaea, which may contribute to the halotherapeutic effects.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"17 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.70095","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143889122","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}

引用次数: 0

Halophilic and Non-Halophilic Microbial Communities in Relation to Physico-Chemical Characteristics of Salt Mine Air 与盐矿空气理化特性相关的嗜盐与非嗜盐微生物群落

IF 3.6 4区生物学

Environmental Microbiology Reports Pub Date : 2025-04-30 DOI: 10.1111/1758-2229.70095

Aleksandra Puławska, Jolanta Kalinowska, Michalina Rachubik, Dominika Drzewiecka, Luciana Albuquerque, Conceiçao Egas, Krzysztof Krawczyk, Maciej Manecki, Camille Locht, Magdalena Kowalewicz-Kulbat

{"title":"Halophilic and Non-Halophilic Microbial Communities in Relation to Physico-Chemical Characteristics of Salt Mine Air","authors":"Aleksandra Puławska, Jolanta Kalinowska, Michalina Rachubik, Dominika Drzewiecka, Luciana Albuquerque, Conceiçao Egas, Krzysztof Krawczyk, Maciej Manecki, Camille Locht, Magdalena Kowalewicz-Kulbat","doi":"10.1111/1758-2229.70095","DOIUrl":"https://doi.org/10.1111/1758-2229.70095","url":null,"abstract":"Salt mines are often used for halotherapy against lung and skin diseases. In addition to salt, they also contain various types of microorganisms, which remain poorly characterised. Here, we examined culturable halophilic and non-halophilic microbial populations in relation to the physico-chemical characteristics in the air of four different sites of the Bochnia Salt Mine, a popular halotherapy resort in Southern Poland. At the mine entrance, the temperature was highest (20.8°C) and decreased with increasing distance from the entrance (15.5°C at 2671 m from entrance), while humidity increased from 55.9% to 77.0%, as did the NaCl concentration. At the entrance, non-halophilic microorganisms prevailed, especially fungi that grew at 21°C. Halophiles gradually dominated with distance from the entrance, including halophilic archaea that grew at 28°C or 37°C on medium containing 15%, 20%, or 25% NaCl. Seven halophilic archaeal species were identified by 16S rRNA gene sequencing. The frequency of non-halophiles was inversely related to distance from the entrance, humidity, and presence of ions, while the reverse was seen for halophiles. An exception was the site used for halotherapy, where non-halophilic bacteria dominated. Thus, natural salt mines contain a wide variety of non-halophilic and halophilic microorganisms, including archaea, which may contribute to the halotherapeutic effects.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"17 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.70095","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143888875","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}

引用次数: 0

Young maize plants impact the bacterial community in Australian cotton-sown vertisol more than agricultural practices 玉米幼苗对澳大利亚棉花垂直土壤细菌群落的影响大于农业实践

IF 3.6 4区生物学

Environmental Microbiology Reports Pub Date : 2025-04-30 DOI: 10.1111/1758-2229.13322

Luc Dendooven, Daniel Ramírez-Villanueva, Vanessa Romero-Yahuitl, Karla E. Zarco-González, Nilantha Hulugalle, Viliami Heimoana, Nele Verhulst, Bram Govaerts, Yendi E. Navarro-Noya

{"title":"Young maize plants impact the bacterial community in Australian cotton-sown vertisol more than agricultural practices","authors":"Luc Dendooven, Daniel Ramírez-Villanueva, Vanessa Romero-Yahuitl, Karla E. Zarco-González, Nilantha Hulugalle, Viliami Heimoana, Nele Verhulst, Bram Govaerts, Yendi E. Navarro-Noya","doi":"10.1111/1758-2229.13322","DOIUrl":"https://doi.org/10.1111/1758-2229.13322","url":null,"abstract":"Changes in soil characteristics due to varying farming practices can modify the structure of bacterial communities. However, it remains uncertain whether bacterial groups that break down organic material are similarly impacted. We examined changes in the bacterial community by pyrosequencing the 16S rRNA gene when young maize plants, their neutral detergent fibre fraction, or urea were applied to an Australian Vertisol. This soil was managed with either conventional tillage with continuous cotton, minimum tillage with continuous cotton, or a wheat-cotton rotation. The soil organic carbon content was 1.4 times higher in the wheat-cotton rotation than in the conventional tillage with continuous cotton treatment. Approximately 41.6% of the organic carbon was added with maize plants, and 13.1% of the neutral detergent fibre fraction was mineralized after 28 days. The application of young maize plants and the neutral detergent fibre fraction significantly altered the bacterial community and the presumed metabolic functional structure, but urea did not. Many bacterial groups, such as Streptomyces, Nocardioides, and Kribbella, and presumed metabolic functions were enriched by the application of organic material, but less so by urea. We found that a limited number of bacterial groups and presumed metabolic functions were affected in an irrigated Vertisol by the different cotton farming systems, but many were strongly affected by the application of maize plants or its neutral detergent fibre.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"17 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13322","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143889120","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}

引用次数: 0

More Than a Stick in the Mud: Eelgrass Leaf and Root Bacterial Communities Are Distinct From Those on Physical Mimics 不仅仅是泥里的一根棍子：大叶草的叶子和根的细菌群落不同于那些物理模拟

IF 3.6 4区生物学

Environmental Microbiology Reports Pub Date : 2025-04-30 DOI: 10.1111/1758-2229.70086

Melissa R. Kardish, John J. Stachowicz

引用次数: 0

More Than a Stick in the Mud: Eelgrass Leaf and Root Bacterial Communities Are Distinct From Those on Physical Mimics 不仅仅是泥里的一根棍子：大叶草的叶子和根的细菌群落不同于那些物理模拟

IF 3.6 4区生物学

Environmental Microbiology Reports Pub Date : 2025-04-30 DOI: 10.1111/1758-2229.70086

Melissa R. Kardish, John J. Stachowicz

引用次数: 0

Young maize plants impact the bacterial community in Australian cotton-sown vertisol more than agricultural practices 玉米幼苗对澳大利亚棉花垂直土壤细菌群落的影响大于农业实践

IF 3.6 4区生物学

Environmental Microbiology Reports Pub Date : 2025-04-30 DOI: 10.1111/1758-2229.13322

Luc Dendooven, Daniel Ramírez-Villanueva, Vanessa Romero-Yahuitl, Karla E. Zarco-González, Nilantha Hulugalle, Viliami Heimoana, Nele Verhulst, Bram Govaerts, Yendi E. Navarro-Noya

{"title":"Young maize plants impact the bacterial community in Australian cotton-sown vertisol more than agricultural practices","authors":"Luc Dendooven, Daniel Ramírez-Villanueva, Vanessa Romero-Yahuitl, Karla E. Zarco-González, Nilantha Hulugalle, Viliami Heimoana, Nele Verhulst, Bram Govaerts, Yendi E. Navarro-Noya","doi":"10.1111/1758-2229.13322","DOIUrl":"https://doi.org/10.1111/1758-2229.13322","url":null,"abstract":"Changes in soil characteristics due to varying farming practices can modify the structure of bacterial communities. However, it remains uncertain whether bacterial groups that break down organic material are similarly impacted. We examined changes in the bacterial community by pyrosequencing the 16S rRNA gene when young maize plants, their neutral detergent fibre fraction, or urea were applied to an Australian Vertisol. This soil was managed with either conventional tillage with continuous cotton, minimum tillage with continuous cotton, or a wheat-cotton rotation. The soil organic carbon content was 1.4 times higher in the wheat-cotton rotation than in the conventional tillage with continuous cotton treatment. Approximately 41.6% of the organic carbon was added with maize plants, and 13.1% of the neutral detergent fibre fraction was mineralized after 28 days. The application of young maize plants and the neutral detergent fibre fraction significantly altered the bacterial community and the presumed metabolic functional structure, but urea did not. Many bacterial groups, such as Streptomyces, Nocardioides, and Kribbella, and presumed metabolic functions were enriched by the application of organic material, but less so by urea. We found that a limited number of bacterial groups and presumed metabolic functions were affected in an irrigated Vertisol by the different cotton farming systems, but many were strongly affected by the application of maize plants or its neutral detergent fibre.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"17 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.13322","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143888877","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}

引用次数: 0

Community-Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach 基于监督机器学习方法的亚马逊雨林土地利用变化后社区水平代谢变化

IF 3.6 4区生物学

Environmental Microbiology Reports Pub Date : 2025-04-23 DOI: 10.1111/1758-2229.70088

Md Abdul Wadud Khan, Brendan J. M. Bohannan, Kyle M. Meyer, Ann M. Womack, Klaus Nüsslein, James P. Grover, Jorge L. Mazza Rodrigues

{"title":"Community-Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach","authors":"Md Abdul Wadud Khan, Brendan J. M. Bohannan, Kyle M. Meyer, Ann M. Womack, Klaus Nüsslein, James P. Grover, Jorge L. Mazza Rodrigues","doi":"10.1111/1758-2229.70088","DOIUrl":"https://doi.org/10.1111/1758-2229.70088","url":null,"abstract":"The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long-term established pastures in the Amazon. Machine learning-derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein-coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein-coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long-term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long-term established pastures with implications for the C and N cycles.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"17 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.70088","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865972","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}

引用次数: 0

Community-Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach 基于监督机器学习方法的亚马逊雨林土地利用变化后社区水平代谢变化

IF 3.6 4区生物学

Environmental Microbiology Reports Pub Date : 2025-04-23 DOI: 10.1111/1758-2229.70088

Md Abdul Wadud Khan, Brendan J. M. Bohannan, Kyle M. Meyer, Ann M. Womack, Klaus Nüsslein, James P. Grover, Jorge L. Mazza Rodrigues

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引用次数: 0