Review
Soil Science
Murase Jun, Asiloglu Rasit
Summary: This review focuses on the often overlooked diversity and ecology of protists in wetland rice field soils. Protists with different ecological functions, such as phagotrophs, phototrophs, saprotrophs, and parasites, adapt to a wide range of oxygen tensions and redox potential in the soil. Agricultural managements like fertilization and char application also influence the protist community. Rice roots are a hot spot for protists, as they control the rhizospheric bacterial community and can enhance nutrient release and alter bacterial activities, thereby potentially increasing plant productivity. This review highlights the essential roles of protists in wetland rice field soils and calls for further research on their diversity and functions in this unique agroecosystem.
BIOLOGY AND FERTILITY OF SOILS
(2023)
Article
Multidisciplinary Sciences
Huixin Li, Yanpeng Xu, Yang Wang, Yihao Cui, Jiake Lin, Yuemin Zhou, Shuling Tang, Ying Zhang, Haibin Hao, Zihao Nie, Xiaoyu Wang, Ruikang Tang
Summary: Researchers have developed a bioartificial organism that can scavenge pathogenic waterborne viruses by integrating a semiartificial and specific virus-scavenging organelle. Material-based tactics have attracted extensive attention in driving the functional evolution of organisms.
NATURE COMMUNICATIONS
(2023)
Article
Engineering, Environmental
Jingyan Zhao, Liping Yang, Xiaojing Yang, Xv Zhao, Minghui Li, Shuyan Zhao, Lingyan Zhu, Jingjing Zhan
Summary: 8:2 FTCA can be efficiently absorbed and transformed into other organic compounds in wheat and pumpkin plants, with cytochrome P450 and glutathione-S-transferase playing important roles in the transformation process.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Soil Science
Rasit Asiloglu, Solomon Oloruntoba Samuel, Bahar Sevilir, Muhittin Onur Akca, Pinar Acar Bozkurt, Kazuki Suzuki, Jun Murase, Oguz Can Turgay, Naoki Harada
Summary: This study found that the application of biochar to soil resulted in an increase in the relative abundance of Stramenopiles, mainly oomycetes, in the rice husk biochar amendment, while the poultry litter biochar increased the relative abundances of Amoebozoa, Alveolata, and Excavata. Additionally, among functional groups, the poultry litter biochar increased the relative abundance of phagotrophic protists, while the relative abundance of plant pathogens was decreased by both the rice husk and poultry litter biochar amendments.
BIOLOGY AND FERTILITY OF SOILS
(2021)
Article
Engineering, Chemical
Kamil Janiak, Agnieszka Trusz, Stanislaw Miodonski, Mateusz Muszynski-Huhajlo, Krzysztof Ratkiewicz, Bartosz Zieba, Anna Jurga, Joanna Struk-Sokolowska, Piotr Ofman
Summary: Bacterial mortality is a key parameter for highly efficient wastewater treatment methods. Protozoa are known to feed on bacteria and can affect the efficiency of treatment processes. This study aimed to find an effective method to remove protozoa from activated sludge without impacting overall treatment efficiency.
SEPARATION AND PURIFICATION TECHNOLOGY
(2023)
Article
Environmental Sciences
Zhengjun Feng, Huizhi Ren, Huiping Song, Yan Zou, Miroslav Vosatka, Shaobin Huang, Hainan Lu, Fangqin Cheng
Summary: This study investigated the effects of AMF on plant growth, Pb translocation, and bacteria community in rhizosphere and non-rhizosphere soils spiked with Pb. The results showed that AMF significantly increased the uptake of Pb by Paspalum notatum, and the concentration of soil exchangeable Pb was significantly reduced after plant cultivation, with further reduction observed with AMF application. The majority of the original exchangeable Pb was transformed into stabilized forms. The bacteria community exhibited differences between rhizosphere and non-rhizosphere soils, and both AMF and Pb were stronger impact factors affecting the beta-diversity of soil bacteria community than rhizosphere.
WATER AIR AND SOIL POLLUTION
(2023)
Article
Agriculture, Multidisciplinary
Keke Dang, Jinfeng Hou, Hong Liu, Junwei Peng, Yang Sun, Jiangang Li, Yuanhua Dong
Summary: In this study, the changes in rhizobacteria, endobacteria, and root exudates during the pathogenesis of bacterial wilt in ginger caused by Ralstonia solanacearum (Rs) were analyzed using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS). The results showed that Rs infection led to a 50.00% incidence of bacterial wilt in ginger and altered the composition of bacterial communities in both the endosphere and rhizosphere. Furthermore, the changes in rhizobacterial composition induced corresponding changes in endobacterial and root exudate compositions. The upregulated exudates inhibited ginger bacterial wilt, indicating that ginger produces antibacterial compounds as a defense mechanism against bacterial pathogens.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Veterinary Sciences
Juan Manuel Palma-Hidalgo, David R. Yanez-Ruiz, Elisabeth Jimenez, A. Ignacio Martin-Garcia, Alejandro Belanche
Summary: The study found that rearing newborn goat kids in contact with adult companions promoted rumen microbial development, leading to better physiological development prior to weaning.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
John T. Lisle, George Lukasik
Summary: This study investigated the inactivation rates of MS2, PV1, and C. parvum in an anaerobic and reduced groundwater system. The results showed that the geochemical conditions in the aquifer enhanced the inactivation rates of the microorganisms, providing a natural way to reduce concentrations of microbial indicators and pathogens of human health concern in injected surface water.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Yingwen Mai, Jianyi Zheng, Jiaxiong Zeng, Zihe Wang, Fei Liu, Lu Ma, Min Zhou, Shanshan Zhao, Bo Wu, Cheng Wang, Qingyun Yan, Zhili He, Longfei Shu
Summary: The growth and fate of protozoa and associated bacteria in drinking water systems have been neglected, and disinfection methods have little effect on them. Ultrafiltration membranes unexpectedly serve as an ideal growth surface for protozoa and promote the growth of associated bacteria. This poses an emerging health risk in drinking water biosafety.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Microbiology
Xiangnan Zeng, Xin Zhang, Bo Peng, Bingyue Xie, Yuan Yuan, Hui Yao, Xiangwei You, Jianyu Wei, Yiqiang Li
Summary: This study demonstrates that the combined application of Bacillus amyloliquefaciens CAS02 and chitooligosaccharide (COS) significantly improves the control effect against tobacco black shank through multiple pathways, providing a promising strategy for the efficient green control of this devastating disease.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biology
Amy Newman, Emma Picot, Sian Davies, Sally Hilton, Isabelle A. Carre, Gary D. Bending
Summary: Aberrant function of plant circadian clock can lead to altered rhythmicity of rhizosphere bacteria and fungi, resulting in changes in the composition of rhizosphere microbiome with potential consequences for plant health.
Article
Microbiology
Muhammad Saqlain Zaheer, Hafiz Haider Ali, Muhammad Arslan Iqbal, Kehinde O. Erinle, Talha Javed, Javaid Iqbal, Makhdoom Ibad Ullah Hashmi, Muhammad Zahid Mumtaz, Ehab A. A. Salama, Hazem M. Kalaji, Jacek Wrobel, Eldessoky S. Dessoky
Summary: Plant growth-promoting rhizobacteria (PGPR) associate with cereal crops and exert their function by synthesizing phytohormones such as cytokinin to promote plant growth. In this experiment, wheat seeds were inoculated with rhizobacterial strains that either produced or did not produce cytokinin. The results showed that the cytokinin-producing strain significantly improved wheat growth and yield-related parameters compared to the strain that did not produce cytokinin. The activity of enzymes, proline contents, and endogenous hormonal levels in wheat kernels were also improved with the cytokinin-producing strain. These findings suggest that microbial cytokinin production is necessary for stimulating plant growth and activating antioxidant and physiological systems in wheat.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Sirui Wang, Tiantian Zhou, Hewen Zhao, Kezhong Zhang, Jinteng Cui
Summary: We studied the rhizosphere microenvironment of Rhododendron mucronulatum in Beijing's Yunmeng Mountain National Forest Park and found significant changes in soil physicochemical properties and enzyme activities. The rhizosphere bacterial diversity was higher in the flowering period and was not influenced by elevation. Rhizomicrobium was the dominant genus in both periods, but its abundance decreased in the deciduous period, potentially influencing the rhizosphere bacterial community.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Plant Sciences
Xianheng Fu, Qi Fu, Xiaozheng Zhu, Xian Yang, Huaihai Chen, Shiqing Li
Summary: The aim of this study was to examine the role of microdiversity in influencing the distribution of rhizosphere-associated microbial species across environmental gradients. The results showed that bacteria exhibited rich microdiversity, while fungi showed low microdiversity. Different ecotypes within bacterial OTUs were found to be positively or negatively associated with environmental factors.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Soil Science
Jessica Clayton, Kathleen Lemanski, Michael Bonkowski
Summary: The study found significant shifts in soil microbial stoichiometry and metabolic quotient after reaching a critical threshold of 1% organic carbon. Increasing organic carbon led to higher microbial nitrogen and decreased metabolic quotient, which remained constant at a low level thereafter. Soils with low organic carbon had unstable microbial fractions, while exceeding the threshold value led to a new equilibrium state allowing for more efficient carbon acquisition by soil microbes.
BIOLOGY AND FERTILITY OF SOILS
(2021)
Article
Microbiology
Samira Khanipour Roshan, Kenneth Dumack, Michael Bonkowski, Peter Leinweber, Ulf Karsten, Karin Glaser
Summary: The study found significant differences in cercozoan and endomyxan communities in biocrusts from different habitats, with distinct taxonomic compositions and functional roles.
Article
Microbiology
Robin-Tobias Jauss, Anne Nowack, Susanne Walden, Ronny Wolf, Stefan Schaffer, Barbara Schellbach, Michael Bonkowski, Martin Schlegel
Summary: Through air sample analysis, we found that Cercozoa and Oomycota have rich biodiversity in forests, and their dispersal is not spatially restricted, with plant pathogens even coming from outside the forest.
EUROPEAN JOURNAL OF PROTISTOLOGY
(2021)
Article
Environmental Sciences
Christoph Rosinger, Michael Bonkowski
Summary: Studies have shown that freeze-thaw events have significant impacts on soil microbial communities and biogeochemical processes, with various environmental factors influencing soil responses. High-carbon soils are more susceptible to microbial biomass losses compared to low-carbon soils, and soil age plays a larger role in determining soil chemical and microbial responses to freeze-thaw events than organic carbon content.
Article
Agronomy
A. Schnepf, A. Carminati, M. A. Ahmed, M. Ani, P. Benard, J. Bentz, M. Bonkowski, M. Knott, D. Diehl, P. Duddek, E. Kroner, M. Javaux, M. Landl, E. Lehndorff, E. Lippold, A. Lieu, C. W. Mueller, E. Oburger, W. Otten, X. Portell, M. Phalempin, A. Prechtel, R. Schulz, J. Vanderborght, D. Vetterlein
Summary: This study investigates the importance and interconnectedness of rhizosphere processes across multiple scales using modeling and experimental methods. The results demonstrate the use of various modeling tools to explain the spatial and temporal distribution of rhizosphere components and show how different scales and processes can be linked.
Article
Zoology
Mona van Schingen-Khan, Leon Marian Fynn Barthel, Dung Thi Kim Pham, Cuong The Pham, Truong Quang Nguyen, Thomas Ziegler, Michael Bonkowski
Summary: Climate change negatively impacts vertebrate biodiversity, especially tropical lizards with narrow temperature tolerances. The crocodile lizard, an ecologically specialized species, is at risk of extinction due to habitat loss and overharvesting. This study uses temperature data to assess the species' vulnerability and provides insights into its temperature preferences and seasonal variations, offering guidance for conservation measures.
Article
Microbiology
Julien Roy, Florent Mazel, Kenneth Dumack, Michael Bonkowski, Matthias C. Rillig
Summary: The study demonstrated that the assembly of soil Cercozoa community at the field scale is mainly driven by niche-based processes influenced by evolutionary legacy of adaptation to conditions primarily related to the soil compartment, giving a deeper understanding of the selection pressures that shaped their evolution.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Entomology
Jonathan Hense, Karsten Schittek, Markus Forbrigerc, Bertil Maechtle, Frank Schaebitz, Michael Bonkowski
Summary: An investigation was conducted on the oribatid mites in a high-Andean cushion peatland in southern Peru. A total of 17 species belonging to eight families were identified in five microhabitats. The rarefaction analysis showed a potential maximum of 18 taxa per 1000 specimens in this peatland site. The abundance analysis revealed the dominance of three species, the subdominance of five species, and the occurrence of three recedent, two subrecedent, and four sporadic taxa. The average abundance of oribatid mites was 3.0 specimens/cm <(-3)(SD = 5.9). However, significantly higher densities were found in muddy soils and sparsely vegetated areas compared to soils covered by dense vegetation cushions. The identification of deposited and damaged remains of oribatid mites is also discussed.
Article
Environmental Sciences
Oscar Rindt, Christoph Rosinger, Michael Bonkowski, Christian Rixen, Nicolas Brueggemann, Tim Urich, Anna Maria Fiore-Donno
Summary: A study in the Central Alps found that the microbial biomass and dissolved C in the soil increased during snowmelt and from spring to summer. The absence of soil freezing in winter and the rise in dissolved C supported a continued growth of the microbial biomass, without any sudden collapse. These findings highlight the importance of the insulating effect of seasonal snow cover for microbial dynamics.
Article
Plant Sciences
Lioba Rueger, Minh Ganther, Jule Freudenthal, Jan Jansa, Anna Heintz-Buschart, Mika Tapio Tarkka, Michael Bonkowski
Summary: Plants have a significant impact on the development of microbial communities in their rhizosphere, and the role of root caps and specific root zones in microbial community assembly is still unclear. In this study, the composition of prokaryote and protist microbiomes along maize roots was compared between intact and decapped roots, as well as between wild type and root hairless mutant. The absence of root caps had a stronger effect on microbiome composition than the absence of root hairs, affecting microbial community composition at older root zones and higher trophic levels.
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
Jannik Martens, Carsten W. Mueller, Prachi Joshi, Christoph Rosinger, Markus Maisch, Andreas Kappler, Michael Bonkowski, Georg Schwamborn, Lutz Schirrmeister, Janet Rethemeyer
Summary: In Siberian permafrost sediments deposited during the Pleistocene, the presence of reactive iron leads to the mineral-bound organic carbon, which reduces microbial CO2 production after thawing. Rapid thaw of ice-rich Pleistocene-age permafrost can expose a large pool of organic matter to microbial degradation and greenhouse gas emissions, but protective physico-chemical mechanisms may restrict microbial accessibility and reduce decomposition, influenced by changing environmental conditions during sediment deposition. Study of different organic matter fractions in Siberian permafrost deposited during colder and warmer periods reveals that carbon preservation in mineral-associated organic matter is enhanced by reactive iron minerals, while warmer and wetter conditions reduce organic matter stabilization and increase CO2 production. The stability and bioavailability of Pleistocene-age permafrost carbon are important for predicting future climate-carbon feedback.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
Thi Bao-Anh Nguyen, Michael Bonkowski, Kenneth Dumack, Qing-Lin Chen, Ji-Zheng He, Hang-Wei Hu
Summary: This study investigated the response of antibiotic resistance genes (ARGs) in soil to predation pressure from protists. The results showed that an increase in protistan predation pressure was associated with higher abundance and diversity of ARGs in the soil. High concentrations of protists significantly increased the abundance of genes encoding multidrug and tetracycline resistance, as well as the abundance of certain bacterial genera.
Article
Environmental Sciences
Christoph Rosinger, Johannes Rousk, Michael Bonkowski, Janet Rethemeyer, Andrea Jaeschke
Summary: Extreme environmental conditions in the Atacama Desert make it one of the most inhospitable habitats for life on Earth. This study investigated the physiological responses of soil microorganisms to a simulated precipitation event in these extreme soils. The results revealed that microbial growth did occur following rewetting, although at much lower rates compared to other soil systems. Carbon supplementation increased bacterial growth and respiration responses, indicating a carbon-limited microbial community. The study also found evidence of an active archaeal community in the hyper-arid soils upon rewetting.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Susanne Walden, Robin-Tobias Jauss, Kai Feng, Anna Maria Fiore-Donno, Kenneth Dumack, Stefan Schaffer, Ronny Wolf, Martin Schlegel, Michael Bonkowski
Summary: Tree canopies are colonized by billions of highly specialized microorganisms adapted to variable microclimatic conditions. The study found distinct seasonality patterns in tree canopy protists, with different taxa in spring and autumn, and a dominance of bacterivores and omnivores in tree crowns. Surprisingly, endomyxan root pathogens were abundant in tree canopies during autumn, suggesting a potential role of the canopy surface as a physical filter for air-dispersed propagules.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Soil Science
C. Beraud, F. Piola, J. Gervaix, G. Meiffren, C. Creuze des Chatelliers, A. Delort, C. Boisselet, S. Poussineau, E. Lacroix, A. A. M. Cantarel
Summary: This study investigated the soil factors influencing the development of biological denitrification inhibition (BDI) and found that initial soil moisture, ammonium concentration, and the initial abundance of certain microbial genes play significant roles in BDI development. Additionally, the research highlighted the relevance of biotic factors in explaining BDI and proposed the use of procyanidin concentration from plant belowground system as a new proxy for measuring BDI intensity.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Yizhu Qiao, Tingting Wang, Qiwei Huang, Hanyue Guo, He Zhang, Qicheng Xu, Qirong Shen, Ning Ling
Summary: Soil microbial community coalescence, the mixing and interaction of microbial communities, has been found to enhance the stability and complexity of rhizobacterial networks, leading to improved plant health and biomass. This study investigated the effects of different degrees of bacterial community coalescence on plant disease resistance by mixing soils from healthy and diseased habitats for watermelon planting. The results showed that mixing in more healthy soil reduced the plant disease index and increased biomass by improving the stability and complexity of the rhizobacterial network. Core taxa Nitrospirillum and Singulisphaera were enriched in the rhizosphere from healthy soils and played important roles in disease suppression and regulating the positive cohesion and modularity of the networks. Overall, these findings provide insights into the potential mechanism of microbial community coalescence for improving plant microbial community function and suggest new tools for enhancing plant fitness via soil microbiota mixing.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Mengqiu He, Shending Chen, Lei Meng, Xiaoqian Dan, Wenjie Wang, Qinying Zhu, Zucong Cai, Jinbo Zhang, Pierfrancesco Nardi, Christoph Mueller
Summary: Maize genotypes directly affect gene expression and nitrogen uptake capacity. The feedback between maize genotypes and soil nitrogen transformations, as well as their regulations on nitrogen uptake capacity, have been studied. The findings suggest that maize genotypes play a central role in regulating these feedbacks, which are important for maize breeding and enhancing maize production.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
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
Soil Science
Sensen Chen, Ying Teng, Yongming Luo, Eiko Kuramae, Wenjie Ren
Summary: This study comprehensively assesses the effects of NMs on the soil microbiome through a global meta-analysis. The results reveal significant negative impacts of NMs on soil microbial diversity, biomass, activity, and function. Metal NMs, especially Ag NMs, have the most pronounced negative effects on various soil microbial community metrics.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Shareen K. D. Sanders, Gerard Martinez-De Leon, Ludovico Formenti, Madhav P. Thakur
Summary: Collembolans, the diverse group of soil invertebrates, are affected by anthropogenic climate warming, which alters their diversity and density. In addition to abiotic stressors, changes in food availability, specifically the abundance of saprotrophic and mycorrhizal fungi, influence Collembola responses to climate warming. Collembolans prefer saprotrophic fungi but rely on mycorrhizal fungi when food sources are scarce. Understanding the mechanisms behind these dietary shifts in warm-dry and warm-wet soil conditions is crucial for predicting the impact of climate change on Collembola-fungal interactions.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Wimonsiri Pingthaisong, Sergey Blagodatsky, Patma Vityakon, Georg Cadisch
Summary: A study found that mixing high-C/N ratio rice straw with low-C/N ratio groundnut stover can improve the chemical composition of the input, stimulate microbial growth, decrease the loss of residue-derived carbon in the soil, and reduce native soil carbon and nitrogen consumption.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Jiachen Wang, Jie Zhao, Rong Yang, Xin Liu, Xuyuan Zhang, Wei Zhang, Xiaoyong Chen, Wende Yan, Kelin Wang
Summary: Nitrogen is vital for ecosystem productivity, restoration, and succession processes. This study found that legume intercropping was more effective than chemical nitrogen fertilizers in promoting the complexity and stability of the soil micro-food web, as it increased microbial and nematode communities and enhanced energy flow patterns.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
