Article
Environmental Sciences
Wu Xiong, Alexandre Jousset, Rong Li, Manuel Delgado-Baquerizo, Mohammad Bahram, Ramiro Logares, Benjamin Wilden, Gerard Arjen de Groot, Nathalie Amacker, George A. Kowalchuk, Qirong Shen, Stefan Geisen
Summary: The study examined 38 sequence-based datasets of paired bacterial and protistan taxa from a variety of habitats. It found that microbiomes in soils were the most diverse, with predatory protists dominating, while aquatic environments were characterized by phototrophic protists. The study also highlighted the impact of anthropogenic factors on the trophic structure of microbiomes, suggesting a reduction in higher trophic complexity in human-influenced environments.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Microbiology
Andrew Dopheide, Carina Davis, Jonathan Nunez, Graeme Rogers, David Whitehead, Gwen-Aelle Grelet
Summary: The study revealed that the biodiversity of fungi, protists, and nematodes in deep agricultural soil decreases with depth, and deep soil organisms are not simply subsets of surface organisms, with some unique species existing only in deep soil. Additionally, deep soil communities are more concentrated around scarce resources niches, as shown by differences in co-occurrence network structures.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Ecology
Camila Duarte Ritter, Dominik Forster, Josue A. R. Azevedo, Alexandre Antonelli, R. Henrik Nilsson, Martha E. Trujillo, Micah Dunthorn
Summary: The study utilized DNA metabarcoding data to explore co-occurrence patterns of microorganisms in different Amazonian habitats, revealing that most operational taxonomic units (OTUs) were bacteria with various metabolism modes, and a high frequency of saprotrophic fungi. Organic carbon and base saturation indices were important in Amazonian co-occurrence networks, while other soil properties played a role in co-exclusion. Different habitats showed similar network properties with variations in modularity, likely due to flooding events.
Article
Ecology
Haojie Su, Yuhao Feng, Jianfeng Chen, Jun Chen, Suhui Ma, Jingyun Fang, Ping Xie
Summary: The study found that fish have negative impacts on zooplankton and water clarity while having positive effects on primary producers and water nutrients in freshwater ecosystems. Additionally, factors such as eutrophication, warming, and predator abundance strengthen trophic cascade effects.
Article
Soil Science
Lioba Rueger, Kai Feng, Yan Chen, Ruibo Sun, Bo Sun, Ye Deng, Doris Vetterlein, Michael Bonkowski
Summary: Soil texture is critical to root growth and plays a significant role in the occurrence and distribution of soil microbiota. This study investigated the influence of soil texture on root morphology and the rhizosphere microbial composition of maize. The results showed a linear relationship between soil texture and root morphology, as well as a stronger selection effect of the rhizosphere in soils with a high sand fraction. This research highlights the importance of soil texture in shaping the rhizosphere microbiome of maize.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Tye L. Kindinger, Jason A. Toy, Kristy J. Kroeker
Summary: Understanding how ocean acidification and warming affect consumption rates of predators and herbivores in marine ecosystems is crucial for predicting responses to global change. Studies show that both OA and warming can directly impact consumers, but there is high variability in consumption rates, likely due to species adaptation and methodological differences. Exposure to OA may reduce consumption rates on average, but rates can increase when both consumers and their resources are exposed to the same conditions concurrently.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Katarzyna Turnau, Edyta Fialkowska, Rafal Wazny, Piotr Rozpadek, Grzegorz Tylko, Sylwia Bloch, Bozena Nejman-Falenczyk, Michal Grabski, Alicja Wegrzyn, Grzegorz Wegrzyn
Summary: Our study revealed a complex trophic network involving predatory fungi armed with bacteria and bacteriophages, as well as the rotifers they prey on. Bacteria and fungi share nutrients obtained from rotifers, and bacteria have the ability to immobilize rotifers. This microbiological puzzle remains largely unknown and requires further exploration.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Microbiology
Stefan Geisen
Summary: Microbes in the soil play a dominant role in the biodiversity of the planet, but there are still some shortcomings in the current research on their diversity. To address these issues, studies on soil microbiomes should be more comprehensive in terms of targeted taxa and resolution, integrate functional information with taxonomic information, and combine temporal analysis with spatial analysis.
Article
Biodiversity Conservation
Owen J. Holland, Mary A. Young, Craig D. H. Sherman, Mun Hua Tan, Harry Gorfine, Ty Matthews, Adam D. Miller
Summary: Rising ocean temperatures are causing declines and range shifts in marine species globally. The direct effects of climate change on marine biology are well documented, but understanding of indirect effects through trophic interactions is limited. Evidence shows ocean warming decoupling critical trophic interactions for an important mollusc in a climate change hotspot.
GLOBAL CHANGE BIOLOGY
(2021)
Article
Ecology
Youssef Yacine, Korinna T. Allhoff, Avril Weinbach, Nicolas Loeuille
Summary: Global warming is severely impacting ecosystems and biodiversity, with fast evolution potentially helping species adapt and survive. However, even with fast evolution, disruptions in food web structure and functioning are inevitable, indicating that reversing warming may not be enough to restore previous ecosystem structures.
JOURNAL OF ANIMAL ECOLOGY
(2021)
Article
Environmental Sciences
Zelong Li, Jing Wang, Jingfeng Fan, Hao Yue, Xiuhong Zhang
Summary: This study investigates the effects of domoic acid (DA) on protistan ecology in marine environments. The results show that trace amounts of DA can alter the diversity of protistan community and have negative effects on consumers and phototrophs. Additionally, the study reveals that DA shapes the protistan ecological network by acting on phototrophs and triggering cascading effects in networks, leading to shifts in ecological succession.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Plant Sciences
Stefan Geisen, Robin Heinen, Elena Andreou, Teun van Lent, Freddy C. ten Hooven, Madhav P. Thakur
Summary: The study found that microbial groups did not affect plant growth and only fungi increased defense compounds in early- and mid-successional forbs. In early successional forbs, shoot biomass-defence relationships were negatively correlated in most microbial treatments, while in mid-successional forbs, they were positively correlated in several microbial treatments. The presence of different microbiomes commonly removed the observed growth-defence relationships.
Article
Environmental Sciences
Rasit Asiloglu
Summary: Biochar applications have significant impacts on the soil microbial community and functionality, but studies on protists, which are an important component of eukaryotic diversity, are currently lacking.
Article
Microbiology
Maria Korneykova, Dmitry Nikitin, Vladimir Myazin
Summary: The soil microbiome of the Barents Sea coast of the Kola Peninsula was characterized for the first time, revealing a significant presence of bacteria, fungi, and archaea. The biomass of microorganisms varied greatly in the soil, with fungi dominating the microbial biomass.
Article
Microbiology
Luis Gonzalez-de-Salceda, Ferran Garcia-Pichel
Summary: This study discovered a 3D non-linear relationship between the number of 16S or 18S RNA genes and cell volume, which is unique in the microbial field. This relationship allows for a simple correction for variations in both copy number per genome and ploidy level in ribosomal gene analyses.
Article
Ecology
Nana Liu, Huifeng Hu, Wenhong Ma, Ye Deng, Dimitar Dimitrov, Qinggang Wang, Nawal Shrestha, Xiangyan Su, Kai Feng, Yuqing Liu, Baihui Hao, Xinying Zhang, Xiaojuan Feng, Zhiheng Wang
Summary: This study assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea in arid regions and found positive correlations among microbial functional groups. Studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights.
Article
Environmental Sciences
Mengyue Sun, Mingcong Li, Yuqi Zhou, Jiai Liu, Wenchong Shi, Xiaoliang Wu, Baohua Xie, Ye Deng, Zheng Gao
Summary: This study investigates the effects of different levels and types of nitrogen deposition on soil microorganisms in coastal wetlands. The results show that nitrogen deposition can increase microbial diversity but high concentrations of NH4NO3 and NH4Cl may decrease it. Different types of nitrogen deposition enhance the deterministic process of community assembly and increase the complexity of microbial co-networks. The study provides new insights into the changes in soil microbial communities caused by long-term nitrogen deposition and their ecological effects.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Engineering, Environmental
Lingzhan Miao, Wanyi Li, Tanveer M. Adyel, Yu Yao, Ye Deng, Jun Wu, Yongqiang Zhou, Yue Yu, Jun Hou
Summary: Plastics in the environment create a unique microorganism habitat called the plastisphere. This study investigates the microbial communities in the plastisphere and their ability to biodegrade non-biodegradable and biodegradable plastics. The results show that biodegradable plastics have higher degradation rates and trigger faster succession of the plastisphere compared to non-biodegradable plastics. Ecological networks reveal that biodegradable plastics attract and retain key microorganisms that enhance biodegradation in freshwater ecosystems.
Article
Microbiology
Yingcheng Wang, Ning Dang, Kai Feng, Junbang Wang, Xin Jin, Shiting Yao, Linlin Wang, Songsong Gu, Hua Zheng, Guangxin Lu, Ye Deng
Summary: This study investigated the relationships between grass productivity and diversity and soil microbes in alpine grasslands. The researchers found that microbial diversity was negatively correlated with grass diversity, but positively correlated with grass productivity. The study also showed that grass formed complex and stable ecological networks with bacterial, archaeal, and fungal species, and the grass-fungal networks were the most robust. Additionally, the connectivity degrees of the grass-microbial network were positively correlated with grass productivity, indicating a positive feedback effect. These findings contribute to our understanding of the regulatory mechanisms between plants and microorganisms in alpine grassland ecosystems.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Linlin Wang, Mingliang Zhao, Xiongfeng Du, Kai Feng, Songsong Gu, Yuqi Zhou, Xingsheng Yang, Zhaojing Zhang, Yingcheng Wang, Zheng Zhang, Qi Zhang, Baohua Xie, Guangxuan Han, Ye Deng
Summary: Wetlands are important sources of methane emissions, and changes in the ecohydrological environment can affect methane emissions from coastal ecosystems. In this study, the researchers investigated the responses of prokaryotic, fungal, and cercozoan communities to inundation and found that inundation significantly altered methane emissions and microbial communities. The interdomain networks among microbial communities revealed that methane-associated prokaryotic and cercozoan organisms were keystone taxa, and environmental factors such as pH and soil nutrients played a role in regulating methane flux.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Shiqing Nie, Zhongwang Jing, Jichen Wang, Ye Deng, Yingshuang Zhang, Zheng Ye, Yuan Ge
Summary: Parkinson's disease (PD) has a strong association with the gut microbiome, but the relationship between the gut microbiome and the severity of PD is not well-studied. This study analyzed fecal samples from newly diagnosed and untreated PD patients and healthy controls to investigate this connection. The results showed that Desulfovibrio was significantly increased in PD patients and positively correlated with disease severity. The study also identified a potential pathogenic mechanism involving Desulfovibrio and excessive hydrogen sulfide production that accelerates PD development.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Environmental Sciences
Xiongfeng Du, Songsong Gu, Zheng Zhang, Shuzhen Li, Yuqi Zhou, Zhaojing Zhang, Qi Zhang, Linlin Wang, Zhicheng Ju, Chengliang Yan, Tong Li, Danrui Wang, Xingsheng Yang, Xi Peng, Ye Deng
Summary: Soil bacterial communities in a coastal area follow a distance-decay relationship and the distribution is influenced by body size. This study collected soil samples from two adjacent ecosystems and found that the entire microbial community, as well as individual taxonomic groups, exhibited distance-decay patterns. The turnover rate of microbial communities was higher in nontidal soils and topsoil, with body size influencing the spatial limitation in nontidal topsoil but not in tidal soils.
ENVIRONMENTAL RESEARCH
(2023)
Article
Environmental Sciences
Ke Shi, Bin Liang, Kai Feng, Daliang Ning, Carolyn R. Cornell, Yanqing Zhang, Wenbin Xu, Min Zhou, Ye Deng, Jiandong Jiang, Tiejun Liu, Aijie Wang, Jizhong Zhou
Summary: Electrostimulated hydrolysis acidification (eHA) is an efficient wastewater pretreatment biotechnology that accelerates the removal of refractory pollutants by affecting microbial interspecies associations. This study investigated the principles of cross-niche microbial associations and community assembly using molecular ecological network and phylogenetic bin-based null model analysis. The results showed that electrostimulation significantly increased the degradation efficiency of organic nitrogen pollutants and altered the microbial community composition and structure. Electroactive bacteria were enriched in the electrode biofilm, while functional degraders were enriched in the planktonic sludge. Electrostimulation also strengthened the synergistic microbial associations between sludge and biofilm members, and deterministic assembly became more important. This study enhances our understanding of the manipulation of sludge microbiomes in engineered wastewater treatment systems.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Soil Science
Lioba Rueger, Kai Feng, Yan Chen, Ruibo Sun, Bo Sun, Ye Deng, Doris Vetterlein, Michael Bonkowski
Summary: Soil texture is critical to root growth and plays a significant role in the occurrence and distribution of soil microbiota. This study investigated the influence of soil texture on root morphology and the rhizosphere microbial composition of maize. The results showed a linear relationship between soil texture and root morphology, as well as a stronger selection effect of the rhizosphere in soils with a high sand fraction. This research highlights the importance of soil texture in shaping the rhizosphere microbiome of maize.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Engineering, Environmental
Zheng Zhang, Jiang Li, Hongjun Li, Linlin Wang, Yuqi Zhou, Shuzhen Li, Zhaojing Zhang, Kai Feng, Ye Deng
Summary: In this study, the biogeographic patterns of microeukaryotic plankton diversity, community structure, and co-occurrence patterns were investigated using environmental DNA methods. The results showed a unimodal pattern of planktonic alpha diversity with latitude, and nutrient-related factors were found to be the main drivers of spatial patterns. Additionally, significant regional biogeographic patterns and potential drivers for planktonic communities were identified, with inorganic nitrogen and heavy metals having the greatest impact. Furthermore, the study revealed that anthropogenic activity factors strongly influenced the networked topology and structure of the planktonic community.
Article
Microbiology
Yi Sun, Hongjun Li, Xiaocheng Wang, Hongbo Li, Ye Deng
Summary: Seaweed cultivation, as an important carbon sink, plays a vital role in controlling global climate change. However, limited studies have focused on the dynamics of bacterioplankton in seaweed cultivation activities.
Article
Agronomy
Huilin Yan, Xueli Zhou, Kaifu Zheng, Songsong Gu, Hao Yu, Kun Ma, Yangan Zhao, Yingcheng Wang, Hua Zheng, Hanjiang Liu, Dejun Shi, Guangxin Lu, Ye Deng
Summary: The application of organic fertilizer has been found to change the microbial community and increase forage biomass in monoculture, but its effects on grass-legume mixtures remain unclear.
Article
Biodiversity Conservation
Yao Guo, Songsong Gu, Kaixuan Wu, Andrew J. Tanentzap, Junqi Yu, Xiangfen Liu, Qianzheng Li, Peng He, Dongru Qiu, Ye Deng, Pei Wang, Zhenbin Wu, Qiaohong Zhou
Summary: Microbes in aquatic environments play a critical role in carbon cycling, but our understanding of how they respond to temperature changes across large regions is limited. In this study, we investigated 47 lakes from different regions in China and found that warmer lakes had lower carbon concentrations and higher carbon utilization compared to colder lakes. The changes in bacterial community composition and core species affected the carbon utilization, suggesting that temperature mediates aquatic carbon cycling by altering the interactions between bacteria and carbon substrates.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Yuxiang Zhao, Zishu Liu, Baofeng Zhang, Jingjie Cai, Xiangwu Yao, Meng Zhang, Ye Deng, Baolan Hu
Summary: Research shows that high temperature can promote mutualism and reduce competition among microbial communities. Genomic analysis and culturing experiments in a composting system with temperature variation (20°C-70°C) reveal that temperature selects for stress-tolerant strains (Thermobifida fusca and Saccharomonospora viridis), and mutualistic interactions emerge between them and other strains through the sharing of cobalamin.
NATURE COMMUNICATIONS
(2023)
Article
Green & Sustainable Science & Technology
Chunge Li, Ye Deng, Jingguo Wang, Weibin Ruan, Shang Wang, Weidong Kong
Summary: Soil phenolic acids, derived from crop residue and root exudates, can impact crop growth and soil microbial community. The study investigated the effects of p-hydroxyphenylacetic acid (HPA) and p-hydroxybenzoic acid (HBA) on soil microbial community in soybean and corn fields. HPA/HBA amendment significantly influenced soil bacterial and fungal community structures. HPA enriched bacteria like Gemmatimonas, Bacillus, and Acidobacteria, while HBA enriched fungi like Penicillium and Aspergillus. This research enhances understanding of the barriers to agricultural production caused by monoculture.
