Article
Engineering, Environmental
Jo De Vrieze, Robert Heyer, Ruben Props, Lieven Van Meulebroek, Karen Gille, Lynn Vanhaecke, Dirk Benndorf, Nico Boon
Summary: This study compared four different microbial community fingerprinting methods for characterizing the full-scale anaerobic digestion microbiome, with cytometric fingerprinting through flow cytometry proving to be a reliable, fast method for holistic monitoring. The complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.
Article
Engineering, Environmental
Hugo B. C. Kleikamp, Denis Grouzdev, Pim Schaasberg, Ramon van Valderen, Ramon van der Zwaan, Roel van de Wijgaart, Yuemei Lin, Ben Abbas, Mario Pronk, Mark C. M. van Loosdrecht, Martin Pabst
Summary: Research shows that different 'omics' techniques can yield different taxonomic results in aerobic granular sludge, which has implications for interpreting nutrient removal processes. However, the genera consistently identified in all techniques cover the majority of the protein biomass, providing a valuable resource for further research.
Article
Microbiology
Miriam Goncalves de Chaves, Luis Fernando Merloti, Leandro Fonseca de Souza, Juliana Heloisa Pine Americo-Pinheiro, Dora Ines Kozusny-Andreani, Fatima Maria de Souza Moreira, Siu Mui Tsai, Acacio Aparecido Navarrete
Summary: This study evaluated the co-occurrence relationships between archaeal taxonomic groups and soil physicochemical characteristics in Amazonian soil under different land use systems. It was found that certain archaeal classes dominated in primary and secondary forests, while others were more prevalent in agricultural systems and pastures. The number of co-occurrences between archaeal groups was lower in secondary forests, agricultural systems, and pastures compared to primary forests. These results suggest that soil texture may play a role in mediating interactions between archaeal groups.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Microbiology
Alexander Meene, Laurin Gierse, Theresa Schwaiger, Claudia Karte, Charlotte Schroeder, Dirk Hoeper, Haitao Wang, Verena Gross, Christine Wuensche, Pierre Muecke, Bernd Kreikemeyer, Martin Beer, Doerte Becher, Thomas C. Mettenleiter, Katharina Riedel, Tim Urich
Summary: This study investigates the structure and function of the archaeome in the porcine intestinal tract during a non-lethal Influenza A virus infection. It reveals significant changes in the abundance and composition of archaea along the ileum and colon, dominated by Methanobrevibacter and Methanosphaera genera. The study also explores the major methanogenesis pathways of these archaea and identifies some effects of the H1N1 infection on the central metabolism of gut archaea.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Environmental Sciences
Kusum Dhakar, Shlomit Medina, Hamam Ziadna, Karam Igbaria, Guy Achdari, Ran Lati, Raphy Zarecki, Zeev Ronen, Guy Dovrat, Hanan Eizenberg, Shiri Freilich
Summary: Microbial communities in different crop fields respond differently to the application of the herbicide atrazine, as revealed by 16S rRNA gene amplicon sequencing. The nutrient-poor soil showed a different response compared to the nutrient-rich soils, both in terms of atrazine persistence and its effect on bacterial community structure and composition. Specific bacterial degraders of atrazine were more abundant in the contaminated nutrient-poor soil, while bacteria involved in nitrogen cycling were more abundant in the contaminated nutrient-rich soil. Understanding these responses can help in designing precision application strategies.
ENVIRONMENTAL RESEARCH
(2023)
Review
Agriculture, Dairy & Animal Science
Margaret D. Weinroth, Aeriel D. Belk, Chris Dean, Noelle Noyes, Dana K. Dittoe, Michael J. Rothrock, Steven C. Ricke, Phillip R. Myer, Madison T. Henniger, Gustavo A. Ramirez, Brian B. Oakley, Katie Lynn Summers, Asha M. Miles, Taylor B. Ault-Seay, Zhongtang Yu, Jessica L. Metcalf, James E. Wells
Summary: Microbiome studies in animal science using 16S rRNA gene sequencing are becoming more common. This review serves as a guide for animal scientists less familiar with this method, discussing common issues and considerations in planning such studies.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Microbiology
Clarisse Marotz, Kellen J. Cavagnero, Se Jin Song, Daniel McDonald, Stephen Wandro, Greg Humphrey, MacKenzie Bryant, Gail Ackermann, Edgar Diaz, Rob Knight
Summary: This study reanalyzed data from a large sample storage study, confirming that 95% ethanol is an effective, practical, and cost-effective preservative that can preserve samples at room temperature for weeks. It also identified the optimal ratio of 95% ethanol to sample in stool and saliva samples, providing a solution that enables crowdsourcing microbiome studies and lowers the barrier for collecting diverse samples.
Article
Soil Science
Jacob Weverka, Gabriel C. Runte, Elizabeth L. Porzig, Chelsea J. Carey
Summary: Soil organic carbon (SOC) is important for soil health and climate change mitigation. Plant and soil microbial communities can serve as indicators of SOC concentrations and future changes. Combining these ecological indicators can improve the prediction of SOC concentration and changes.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Agronomy
Svetlana B. Lysko, Olga A. Baturina, Natalia B. Naumova, Nadezhda A. Lescheva, Valentina I. Pleshakova, Marsel R. Kabilov
Summary: This study examined the effect of pectin prebiotics on the gut microbiota of chickens. The results showed that the prebiotic supplementation increased the abundance of Enterococcus and improved feed use efficiency and growth performance. The response of the microbiota to antibiotics showed more sex-related differential OTUs compared to the pectin prebiotic. Therefore, sex should be taken into account in interventional studies of gut microbiota.
Article
Biotechnology & Applied Microbiology
Dattatray S. Mongad, Nikeeta S. Chavan, Nitin P. Narwade, Kunal Dixit, Yogesh S. Shouche, Dhiraj P. Dhotre
Summary: 16S rRNA gene amplicon sequencing accurately characterizes microbial taxonomic abundances but lacks functional information. MicFunPred, a new tool, uses core genes to predict metagenomes, showing low False Positive Rate and performing faster with lower computational requirements compared to other tools.
Article
Agronomy
Natalia B. Naumova, Tatiana Y. Alikina, Natalia S. Zolotova, Alexey Konev, Valentina Pleshakova, Nadezhda A. Lescheva, Marsel R. Kabilov
Summary: The study found that feed enriched with probiotics can significantly reduce the presence of opportunistic pathogen Escherichia/Shigella, increase duck production performance, and enhance fecal microbial diversity.
Article
Microbiology
Laura Seidel, Elias Broman, Magnus Stahle, Emelie Nilsson, Stephanie Turner, Wouter Hendrycks, Varvara Sachpazidou, Anders Forsman, Samuel Hylander, Mark Dopson
Summary: This study compared an unaffected Baltic Sea bay to a heated bay that has undergone artificial warming for ~50 years, and found that climate change is likely to alter microbial seasonality and diversity in coastal water, resulting in prolonged and increased algae blooming and elevated respiration rates.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Environmental Sciences
Yiwen Huang, Wenjie Ren, Haoran Liu, Huimin Wang, Yongfeng Xu, Yujuan Han, Ying Teng
Summary: This study found that the effect of drying-rewetting cycles on the dissipation of DEHP in different types of soils is mainly derived from microbial degradation in Lou soil, while the interplay between microbial functions and soil attributes contributes to the promotion of DEHP dissipation in Red soil.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Entomology
Ivan Y. Dee Tan, Ma. Anita M. Bautista
Summary: In this study, high-throughput 16S rRNA gene amplicon sequencing and analysis were used to profile bacterial communities in four local silkworm strains reared in the Philippines. The results showed that these strains are abundant in bacteria belonging to the genera Pseudomonas, Sphingomonas, Delftia, Methylobacterium, and Acinetobacter. The study also revealed that bacterial diversity and evenness increase as larvae mature, which can be correlated to larval development and shifts in the amount and age of mulberry leaves consumed.
Article
Environmental Sciences
Paula Alejandra Lamprea Pineda, Kristof Demeestere, Jose Joaquin Gonzalez-Cortes, Allan A. Alvarado-Alvarado, Nico Boon, Frank Devlieghere, Herman Van Langenhove, Christophe Walgraeve
Summary: This study investigated the removal of difficult-to-degrade VOC mixtures using biofiltration and the impact of operational conditions. The results showed that the type of inoculum and packing material influenced the removal efficiency, and different microbial populations dominated in the biofilters.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Ecology
Kunkun Fan, Haiyan Chu, David J. J. Eldridge, Juan J. J. Gaitan, Yu-Rong Liu, Blessing Sokoya, Jun-Tao Wang, Hang-Wei Hu, Ji-Zheng He, Wei Sun, Haiying Cui, Fernando D. D. Alfaro, Sebastian Abades, Felipe Bastida, Marta Diaz-Lopez, Adebola R. R. Bamigboye, Miguel Berdugo, Jose L. Blanco-Pastor, Tine Grebenc, Jorge Duran, Javier G. G. Illan, Thulani P. P. Makhalanyane, Arpan Mukherjee, Tina U. U. Nahberger, Gabriel F. F. Penaloza-Bojaca, Cesar Plaza, Jay Prakash Verma, Ana Rey, Alexandra Rodriguez, Christina Siebe, Alberto L. L. Teixido, Pankaj Trivedi, Ling Wang, Jianyong Wang, Tianxue Yang, Xin-Quan Zhou, Xiaobing Zhou, Eli Zaady, Leho Tedersoo, Manuel Delgado-Baquerizo
Summary: In urban greenspaces, soil biodiversity is positively correlated with multiple ecosystem functions, while plant diversity indirectly influences multifunctionality. Conserving soil biodiversity is crucial for supporting multiple dimensions of ecosystem functioning in urban ecosystems.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Plant Sciences
Meitong Jiang, Manuel Delgado-Baquerizo, Mengting Maggie Yuan, Jixian Ding, Etienne Yergeau, Jizhong Zhou, Thomas W. Crowther, Yuting Liang
Summary: This study found that native microbial strains originating from typical agricultural soils can promote maize growth better than commercial plant growth-promoting rhizobacteria in soils with different fertility. The colonization and positive interaction with resident microbial communities contribute to the superior performance of native strains. These findings suggest that engineering crop microbiomes using native microbes could improve food production in poor soils.
Article
Environmental Sciences
Federica D'Alo, Laura Zucconi, Silvano Onofri, Fabiana Canini, Nicoletta Cannone, Francesco Malfasi, Daniel Kumazawa Morais, Robert Starke
Summary: We studied the response of soil archaeal communities to climate change in Alpine areas and found that warming led to an increase in the abundance of Archaea in snowbeds. This increase was negatively correlated with fungal abundance and micronutrient levels, but positively correlated with soil water content. We also observed an enrichment of certain functions in the transcripts of soil archaea in response to warming. Our findings provide valuable insights into the potential changes in composition and function of soil archaea under climate change.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Environmental Sciences
Tingting Ren, Jiahui Liao, Manuel Delgado-Baquerizo, Juanping Ni, Yuanyuan Li, Long Jin, Honghua Ruan
Summary: Biochar and biogas-slurry inputs significantly enhance the accumulation of soil particulate organic carbon (POC) and total soil organic carbon (SOC).
LAND DEGRADATION & DEVELOPMENT
(2023)
Article
Environmental Sciences
Weiqiang Dou, Bo Xiao, Manuel Delgado-Baquerizo, Daniel Revillini, Giora J. Kidron
Summary: Biocrusts are important components in drylands, supporting soil microbial diversity and carbon stocks. Nitrogen fertilization can indirectly promote soil respiration and carbon losses by increasing microbial richness and diversity, highlighting the need to mitigate land degradation and anthropogenic nitrogen deposition to maintain healthy dryland ecosystems and carbon storage.
LAND DEGRADATION & DEVELOPMENT
(2023)
Article
Plant Sciences
Xue Yang, Manuel Delgado-Baquerizo, Yuxuan Niu, Peter Christie, Ji Chen, Hangwei Hu, Yongliang Chen
Summary: The design of cropping systems plays a critical role in bridging the gap between ecosystem sustainability and commercial profitability. Rotational systems with three harvests within 2 yr have shown great potential in enhancing ecosystem services and minimizing trade-offs among multiple agricultural ecosystem services, resulting in a 'win-win' situation for economics and multiple services.
Article
Biotechnology & Applied Microbiology
Yuanyuan Bao, Yan Ma, Wenjing Liu, Xin Li, Yonghui Li, Peng Zhou, Youzhi Feng, Manuel Delgado-Baquerizo
Summary: Artificial lights play a significant role in the conservation and visiting of cultural relics. This study conducted a two-year in situ experiment to evaluate the impacts of different artificial light wavelengths on the phototrophic microbiome of a Chinese imperial mausoleum. The results showed that green light can reduce the abundance of phototrophic bacteria and their organic acid production, thus contributing to long-term preservation.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Biotechnology & Applied Microbiology
Jan Kuechler, Katharina Willenbuecher, Elisabeth Reiss, Lea Nuss, Marius Conrady, Patrice Ramm, Ulrike Schimpf, Udo Reichl, Ulrich Szewzyk, Dirk Benndorf
Summary: The supplementation of lignocellulose-degrading enzymes can improve biogas production in industrial biogas plants. It is crucial to have reliable methods to assess the structural stability of these enzymes. A mass-spectrometric-based assay was established to monitor the structural integrity of enzymes during anaerobic digestion. The study found low structural stability of lignocellulose-degrading enzymes, consistent with previous observations on biogas content.
FERMENTATION-BASEL
(2023)
Article
Soil Science
Ke Shi, Jiahui Liao, Xiaoming Zou, Han Y. H. Chen, Manuel Delgado-Baquerizo, Zhengming Yan, Tingting Ren, Honghua Ruan
Summary: Through rewilding, microbial extracellular and cellular residues can continuously accumulate in soils and significantly contribute to soil organic carbon sequestration. Extracellular residues are mainly driven by fine root biomass, while cellular residues are mainly driven by soil nitrogen and organic carbon content.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Environmental Sciences
Cuiting Wang, Yuan Sun, Xiaoming Zou, Han Y. H. Chen, Manuel Delgado-Baquerizo, Jingyan Yang, Guobing Wang, Yuwei Liu, Honghua Ruan
Summary: Droughts, intensified by climate change, have significant impacts on forest production. This study conducted a drought experiment in a poplar plantation in China and found that drought affected both aboveground and fine root production. Fine root production was more sensitive to drought stress compared to aboveground production.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Biotechnology & Applied Microbiology
Ingrid E. Meyer Cifuentes, Julius Degenhardt, Meina Neumann-Schaal, Nico Jehmlich, David Kamanda Ngugi, Basak Oeztuerk
Summary: This study investigates the degradation of biodegradable plastics in the aquatic environment and demonstrates the role of microbial communities in this process. The researchers found that the type of polymer determines the community structure and degradation capability, with different polymers resulting in different levels of diversity and degradation activity. The study also identified three enzymes capable of degrading a range of biodegradable polymers, which could have potential biotechnological applications.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Federico Biagioli, Claudia Coleine, Manuel Delgado-Baquerizo, Youzhi Feng, Cesareo Saiz-Jimenez, Laura Selbmann
Summary: This study reanalyzed bacterial and fungal communities of caves worldwide and found that outdoor temperature and rainfall are critical factors in explaining differences in microbial diversity patterns. The study also highlights the opposite preferences of fungal and bacterial diversity in different climatic regions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Biodiversity Conservation
Haoran He, Jingxiong Zhou, Yunqiang Wang, Shuo Jiao, Xun Qian, Yurong Liu, Ji Liu, Ji Chen, Manuel Delgado-Baquerizo, Albert C. Brangari, Li Chen, Yongxing Cui, Haibo Pan, Renmao Tian, Yuting Liang, Wenfeng Tan, Raul Ochoa-Hueso, Linchuan Fang
Summary: This study investigated microbial communities in the semi-arid forest ecosystems of China's Loess Plateau. It was found that the diversity of deep soil microbiota is influenced by aridity, but their functional potential remains relatively stable. The study also highlighted the importance of considering soil depth and moisture in understanding dryland ecosystems under future climate scenarios.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Forestry
Maria Dolores Carmona-Yanez, Manuel Esteban Lucas-Borja, Demetrio Antonio Zema, Xin Jing, Yahya Kooch, Pablo Garrido Gallego, Pedro Antonio Plaza-Alvarez, Guiyao Zhou, Manuel Delgado-Baquerizo
Summary: This study compares the ecosystem structure, properties and functions of four types of forests in Central-Eastern Spain to understand how ecosystem multifunctionality (EMF) is influenced by forest management and stand composition in Mediterranean forests. The results show that forest management primarily affects EMF, leading to a decrease in managed stands compared to unmanaged forests.
TREES-STRUCTURE AND FUNCTION
(2023)
Article
Biodiversity Conservation
Wenliang Ju, Linchuan Fang, Guoting Shen, Manuel Delgado-Baquerizo, Ji Chen, Guiyao Zhou, Dengke Ma, Haijian Bing, Lei Liu, Ji Liu, Xiaolian Jin, Liang Guo, Wenfeng Tan, Evgenia Blagodatskaya
Summary: This study investigates the long-term effects of grazing exclusion on soil microbial communities and nutrient dynamics within soil aggregates in a semiarid grassland. The results show that long-term grazing exclusion reduces microbial diversity and carbon sequestration potential, while medium-term grazing exclusion promotes carbon sequestration and nutrient cycling.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)
