Article
Multidisciplinary Sciences
Tomokazu Konishi, Risako Fujiwara, Tadaaki Saito, Nozomi Satou, Yurie Hayashi, Naoko Crofts, Ikuko Iwasaki, Yoshihisa Abe, Shinpei Kawata, Tatsuya Ishikawa
Summary: This study uses HPLC to analyze the levels of lipoproteins in 55 human serum samples and finds that these levels are distributed lognormally with estimated standard amounts and 95% ranges. Certain lipoprotein classes with narrow ranges could be ideal indicators for specific diseases. Additionally, the study reveals that multiple unhealthy lifestyle habits can significantly increase the levels of specific lipoprotein classes.
Article
Microbiology
Chongwen Qiu, Yuanyuan Bao, Evangelos Petropoulos, Yiming Wang, Zhenfang Zhong, Yaozhi Jiang, Xuhong Ye, Xiangui Lin, Youzhi Feng
Summary: This study investigated the effects of different fertilization methods on soil microbial communities, functional compositions, and rice yield. The results showed that the combined application of chemical fertilizers and organic residues resulted in the highest rice yield. Specific bacterial indicator taxa were found to play important roles in soil enzyme activities and nutrient cycling, which directly and/or indirectly determined the rice yield. This study demonstrated the importance of bacterial indicator communities in sustainable agricultural systems.
Article
Forestry
Minmin Cao, Xiang Zheng, Lina Cui, Fan Wu, Haidong Gao, Jiang Jiang
Summary: The increasing rate of atmospheric nitrogen deposition has a significant impact on the structure and function of ecosystems. This study investigated the response of soil microbial communities in a subtropical forest ecosystem to short-term nitrogen deposition. The results showed that nitrogen deposition significantly altered the composition and richness of soil bacterial communities, while the impact on fungal communities was relatively small. The changes in soil water content, pH, and nitrogen availability were found to be the main factors driving the response of microbial communities to nitrogen deposition.
FOREST ECOLOGY AND MANAGEMENT
(2023)
Article
Soil Science
Chuntao Hong, Qingsong Shao, Wensheng Qin, Jianhong Zhang, Bin Wei, Dengfeng Shen, Bingsong Zheng, Haipeng Guo
Summary: Plants grown in stony soils have better root systems and higher crop yields. Stony soils have a different bacterial community composition, greater bacterial diversity, and abundance of specific bacterial taxa compared to non-stony soils, which may be influenced by soil physicochemical properties. The discriminatory bacterial taxa in stony soils play a key role in shaping the rhizosphere and tuber surface soil bacterial communities, affecting tuber size and related gene pathways crucial for tuber development.
BIOLOGY AND FERTILITY OF SOILS
(2021)
Article
Geosciences, Multidisciplinary
Yu-Te Lin, William B. Whitman, David C. Coleman, Shih-Hao Jien, Hsueh-Ching Wang, Chih-Yu Chiu
Summary: The study found significant differences in bacterial community composition between coniferous forest and grassland soils at the treeline, with correlations to soil pH, organic C, and C/N. Historical vegetation types also had a significant impact on the abundance of certain bacterial groups.
Article
Geosciences, Multidisciplinary
Weibo Kong, Fuyuan Su, Qian Zhang, Satoshi Ishii, Michael J. Sadowsky, Samiran Banerjee, Mingan Shao, Liping Qiu, Xiaorong Wei
Summary: This study in the Loess Plateau of China reveals that soil erosion and deposition have significant impacts on bacterial communities and multifunctionality. Erosion reduces bacterial richness and multifunctionality, but deposition can alleviate these negative effects. The study suggests that sustainable soil management and restoration of degraded lands can benefit from understanding the interactions between erosion, deposition, bacterial communities, and soil multifunctionality.
Article
Infectious Diseases
Ali Heydari, Nick D. Kim, Patrick J. Biggs, Jacqui Horswell, Gerty J. H. P. Gielen, Alma Siggins, Matthew D. Taylor, Collette Bromhead, Barry R. Palmer
Summary: The accumulation of heavy metals in agricultural soil from superphosphate fertilisers can cause soil bacteria to develop resistance to heavy metals and antibiotics. This study investigated the co-selection of heavy metal and antibiotic resistance in uncontaminated soil incubated with cadmium, zinc, and mercury for 6 weeks. The microbial communities exposed to heavy metals were found to differ significantly from the control group across various taxonomic levels.
Article
Soil Science
Andrew Dopheide, Carina Davis, Steve A. Wakelin, David Whitehead, Gwen-Aelle Grelet
Summary: Inputs of carbon to soil can stimulate microbial growth and immobilize excess nitrogen from sources such as livestock urine. However, the effects of carbon inputs on microbial communities under conditions of excess soil nitrogen are still not well understood.
BIOLOGY AND FERTILITY OF SOILS
(2023)
Article
Soil Science
Jaimie R. West, Joseph G. Lauer, Thea Whitman
Summary: Tillage disrupts soil aggregation and affects microbial resource availability and community composition. The study found that tillage homogenized soil bacterial communities and increased the influence of homogenizing dispersal on community assembly. No major differences were observed between bacterial communities in the free and occluded microaggregate fractions.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Engineering, Environmental
Quanlong Wang, Xueying Feng, Yingying Liu, Wenzhi Cui, Yuhuan Sun, Shuwu Zhang, Fayuan Wang
Summary: The study investigated the effects of conventional and biodegradable microplastics (MPs) and multiwall carbon nanotubes (MWCNTs) on soil geochemical properties and bacterial communities. The addition of MPs and MWCNTs changed soil pH, dissolved organic carbon content, NO3--N content, available phosphorus content, and the activities of soil enzymes. Co-exposure to MPs and MWCNTs resulted in decreased soil bacterial diversity.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Biology
Paula Andrea Rugeles-Silva, Jairo Andres Londono, Marina Sanchez de Prager, Jaime Eduardo Munoz Florez, Diana Lopez-Alvarez
Summary: Using molecular characterization methods, soil samples from eight farms were compared. The study found 2 domains, 56 phyla, and 190 classes present in the samples. The most abundant phyla were Proteobacteria, Acidobacteria, and Verrucomicrobia, and 41 nitrogen-fixing and phosphate-dissolving genera were identified.
Article
Microbiology
Junping Liu, Yujie Tang, Jiashu Bao, Hankun Wang, Fangren Peng, Pengpeng Tan, Guolin Chu, Shuai Liu
Summary: Understanding microbial communities associated with bulk and rhizosphere soils is important for forest health and productivity. A study on bacterial and fungal communities in pecan plantation soils revealed differences in community structures between bulk and rhizosphere soils. The rhizosphere soil showed lower fungal diversity and a simpler bacterial network, while the opposite was true for fungi. Keystone species involved in nutrient and carbon cycling were enriched in the healthier rhizosphere soil.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Soil Science
Catherine W. Kamau, Richard van Duijnen, Christoph A. O. Schmid, Helga E. Balazs, Julien Roy, Matthias Rillig, Peter Schroeder, Viviane Radl, Vicky M. Temperton, Michael Schloter
Summary: The 2-year outdoor mesocosm experiment investigated the effects of high carbon amendments (HCAs) and different crop rotation systems on soil bacterial communities using a molecular barcoding approach. Results showed a decrease in bacterial diversity after winter barley harvest in no-HCA and wheat straw treatments, while sawdust application stabilized bacterial diversity but negatively affected yields. Different bacterial phyla showed changes in response to the treatments, with only minor differences between wheat straw-amended and no-HCA control samples.
BIOLOGY AND FERTILITY OF SOILS
(2021)
Article
Environmental Sciences
Bing Fu, Chang Fang, Jun Xia, Sentao Pan, Lei Zhou, Yisheng Peng, Yumeng Yan, Yan Yang, Yinglin He, Shijun Chen, Huirong Yang, Jun Wang
Summary: This study aimed to explore the effects of urbanization on soil bacterial communities in coastal cities and found that Proteobacteria and Acidobacteria were the main phyla. The degree of urbanization was found to be an important factor affecting the soil bacterial communities in a non-linear pattern. Additionally, the bacterial communities in urbanized coastal city soils shared similar metabolic potential. This study improved our understanding of the response of soil bacterial communities to urbanization in subtropical coastal cities and provided a useful strategy for monitoring the ecological risks of soil under urbanization.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Ecology
Dan He, Zhiming Guo, Weijun Shen, Lijuan Ren, Dan Sun, Qing Yao, Honghui Zhu
Summary: Increased nitrogen deposition and changes in precipitation patterns have significant impacts on soil microbial communities in tropical/subtropical forests, particularly on fungal communities. The effects of these environmental changes are more prominent in the dry season and have important consequences for soil processes and ecosystem functions.
Review
Microbiology
David C. Karasz, Anna I. Weaver, Daniel H. Buckley, Roland C. Wilhelm
Summary: Bacteria can regulate cell morphology in response to environmental conditions, adopting a filamentous growth habit to optimize their growth and metabolism in highly variable environments. This trait can impact succession, symbioses, and biogeochemistry in soil environments.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Janani Hariharan, Mallory J. Choudoir, Peter Diebold, Kevin Panke-Buisse, Daniel H. Buckley
Summary: A novel Streptomyces strain, named Streptomyces apricus sp. nov., was isolated from soils in Wisconsin, USA. Genome sequencing revealed that this strain had low similarity to type species of Streptomyces. The results of a polyphasic study confirmed the novelty of this isolate.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Agronomy
Juana Munoz-Ucros, Roland C. Wilhelm, Daniel H. Buckley, Taryn L. Bauerle
Summary: The study found that plants are affected by the legacy effects of drought on the rhizosphere microbiome. This drought legacy was propagated and persisted throughout nine weeks of plant growth, independent of prevailing water stress. Drought-impacted rhizospheres had larger populations of desiccation-tolerant and putatively endophytic taxa with established plant growth promoting capabilities.
Article
Soil Science
Roland C. Wilhelm, Harold M. van Es, Daniel H. Buckley
Summary: The study evaluated the accuracy of using microbiome data to predict soil health metrics, with biological health ratings better predicted than chemical or physical ratings. Models trained at the highest taxonomic resolution were the most accurate, with losses in accuracy resulting from rarefying, sparsity filtering, and aggregating at higher taxonomic ranks.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Soil Science
Roland C. Wilhelm, Laurel Lynch, Tara M. Webster, Steffen Schweizer, Thiago M. Inagaki, Malak M. Tfaily, Ravi Kukkadapu, Carmen Hoeschen, Daniel H. Buckley, Johannes Lehmann
Summary: The persistence of soil organic carbon (SOC) is influenced by soil properties, organic matter quality, and climatic conditions. This study compared the susceptibility of newly formed SOC to mineralization in soils developed under different precipitation regimes. The results showed that the susceptibility of SOC to mineralization was affected by iron content and mineralogy, initial SOC, substrate solubility, and microbial substrate use efficiency.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Microbiology
Janani Hariharan, Daniel H. Buckley
Summary: Dispersal is limited for most microbial taxa, and elevation gradients and habitat preferences play important roles in shaping the biogeography of Streptomyces bacteria.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Bhavya Sridhar, Gregory B. Lawrence, Spencer J. Debenport, Timothy J. Fahey, Daniel H. Buckley, Roland C. Wilhelm, Christine L. Goodale
Summary: Soil microbial community composition is closely related to pH, and liming can have immediate and long-lasting effects on the structure and function of bacterial and fungal communities in acid forest soils.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biodiversity Conservation
Bhavya Sridhar, Roland C. Wilhelm, Spencer J. Debenport, Timothy J. Fahey, Daniel H. Buckley, Christine L. Goodale
Summary: Soil pH is closely related to microbial community structure and function, and this study demonstrates how pH can significantly impact carbon storage in forest soils by influencing the structure of bacterial and fungal communities that drive decomposition.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Elliot W. Jackson, Roland C. Wilhelm, Daniel H. Buckley, Ian Hewson
Summary: This study characterized the RNA virome of 38 echinoderm species from all five classes, revealing the diversity of RNA viruses in echinoderms. The study found that the relative viral representation did not significantly differ between different life stages, with the majority of viral contigs discovered from adult tissue transcriptomes.
JOURNAL OF GENERAL VIROLOGY
(2022)
Article
Cell Biology
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides
Summary: This study used a large-scale comparative genomics approach to discover that small genes are more prevalent in phage genomes than in host prokaryotic genomes. These small genes may have important functions, such as encoding anti-CRISPR proteins and antimicrobial proteins.
Article
Microbiology
Ying Wang, Roland C. Wilhelm, Tami L. Swenson, Anita Silver, Peter F. Andeer, Amber Golini, Suzanne M. Kosina, Benjamin P. Bowen, Daniel H. Buckley, Trent R. Northen
Summary: Microorganisms' life-history strategies have a significant impact on the processing of organic carbon, which in turn influences microbial interactions and carbon cycling in soils. High rrn isolates have a greater potential for resource competition and tend to consume a wider variety and larger quantity of substrates compared to low rrn isolates. By connecting bacterial life-history strategies, genomic traits, and metabolism, this study advances our understanding of the links between bacterial community composition and the transformation of carbon in soils.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Roland C. Wilhelm, Samuel E. Barnett, Tami L. Swenson, Nicholas D. Youngblut, Chantal N. Koechli, Benjamin P. Bowen, Trent R. Northen, Daniel H. Buckley
Summary: Carbon metabolism in soil is poorly understood due to the difficulty in obtaining information about microbial metabolites produced by complex soil communities. Our study demonstrates the use of stable isotope probing (SIP) to track C-13 from supplied carbon sources into metabolite pools and biomass, providing valuable insights into carbon transformation in soils. Our findings show that the metabolism of different carbon sources influences the fate of carbon in soils, highlighting the importance of considering carbon source effects in soil metabolic studies. The use of SIP-metabolomics allows for the identification of metabolite markers of microbial growth, activity, and other aspects of microbial function in soil.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Environmental Sciences
Roland C. Wilhelm, Juana Munoz-Ucros, Fabian Weikl, Karin Pritsch, Marc Goebel, Daniel H. Buckley, Taryn L. Bauerle
Summary: Mixed forest stands exhibit greater drought resistance compared to single-species stands due to complementarity in root ecology and physiology. This study investigates whether differences in the drought resistance of soil microbiomes contribute to this phenomenon. The results indicate that changes in soil moisture primarily affect bacteria, particularly Rhizobiales, while fungi, including ectomycorrhizal fungi, are generally unaffected. The resistance of the soil microbiome is higher in spruce root zones compared to beech root zones, corresponding to the proportions of drought-tolerant and drought-sensitive bacterial taxa. Mixed-species root zones contain a hybrid microbiome associated with both beech and spruce. The relative abundances of soil bacteria closely track moisture gradients and are more predictive of soil water content than other environmental variables.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Samuel E. Barnett, Rob Egan, Brian Foster, Emiley A. Eloe-Fadrosh, Daniel H. Buckley
Summary: Soil microbes play a crucial role in the global carbon cycle, but our understanding of how the carbon cycle operates in soil communities is limited. This is mainly due to the lack of functional genes that define carbon transformations. Through metagenomic stable isotope probing, we linked genomic features of bacteria to their carbon acquisition and growth dynamics in soil. We identified genomic traits that can predict bacterial ecological strategies, providing insights into bacterial interactions with soil carbon.
Article
Ecology
Roland C. Wilhelm, Joseph P. Amsili, Kirsten S. M. Kurtz, Harold M. van Es, Daniel H. Buckley
Summary: Soil microbiomes are influenced by soil conditions and can serve as 'bioindicators' for soil health assessment. However, limited information about most microorganisms hampers our ability to interpret the associations of bioindicators and their utility for management guidance.
ISME COMMUNICATIONS
(2023)