Article
Environmental Sciences
Qintong Li, Ryo Hasezawa, Riho Saito, Kunihiro Okano, Kazuya Shimizu, Motoo Utsumi
Summary: Recirculating aquaculture systems (RAS) play an important role in water quality management and water conservation. This study compared the community structures of micro-ecosystems in RAS systems operated at different temperatures in a marine aquarium. It was found that AOA was the primary nitrifier in the biofilters, and its abundance and diversity were higher in high-temperature samples. NOB showed similar relative abundance patterns to AOA, suggesting a cooperative relationship between the two in the marine RAS system.
Article
Soil Science
Shuling Wang, Yongpeng Zhao, Zhihui Wang, Xueli Lv, Alan L. Wright, Xianjun Jiang
Summary: The discovery of comammox Nitrospira has changed our understanding of soil nitrification and expanded our knowledge of nitrifying microorganisms. This study investigated the contribution of comammox to nitrification in paddy soils by analyzing nitrification rates and quantifying the abundance of nitrifying microorganisms. The results showed that comammox Nitrospira had high abundance even when nitrification was almost stopped, indicating its better adaptation to low temperatures compared to other nitrifiers. The study also found that soil water content influenced the activity of comammox clade A, but not clade B. These findings highlight the importance of comammox Nitrospira in soil nitrification and provide insights into the factors shaping their activity.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Ecology
Emily J. Zakem, Barbara Bayer, Wei Qin, Alyson E. E. Santoro, Yao Zhang, Naomi M. Levine
Summary: This study uses a mechanistic microbial ecosystem model to derive simple expressions for the controls on ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in the deep ocean. It finds that the supply of ammonium, not the traits of AOA or NOB, determines the ammonia and nitrite oxidation rates in the water column, and that the relative yields of AOA and NOB alone set their relative bulk carbon fixation rates.
Article
Environmental Sciences
Preeyaporn Pornkulwat, Eakalak Khan, Sorawit Powtongsook, Wuttichai Mhuantong, Chamorn Chawengkijwanich, Tawan Limpiyakorn
Summary: This study comprehensively investigated the impacts of ammonia and salinity on culturing nitrifying microorganisms and successfully formulated nitrifying cultures for different recirculating aquaculture system (RAS) types. The findings suggest that cultures prepared at low ammonia loading rates are most suitable for various RAS types, while cultures prepared at high ammonia loading rates are dominated by nitrifying microorganisms with low substrate affinity.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biotechnology & Applied Microbiology
Chuan Hao Tan, Yee Phan Yeo, Muhammad Hafiz, Noele Kai Jing Ng, Sujatha Subramoni, Shireen Taj, Martin Tay, Xie Chao, Staffan Kjelleberg, Scott A. Rice
Summary: By conducting metagenomic screening and functional validation of AHL genes in the activated sludge microbial community from the Ulu Pandan wastewater treatment plant in Singapore, functional QS genes LuxI and LuxR were identified, indicating that Nitrospira spp. may be active in the activated sludge community.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Article
Ecology
Markus Krueger, Narendrakumar Chaudhari, Bo Thamdrup, Will A. Overholt, Laura A. Bristow, Martin Taubert, Kirsten Kuesel, Nico Jehmlich, Martin von Bergen, Martina Herrmann
Summary: The study reveals that complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in oligotrophic carbonate rock aquifers, due to their ecophysiological characteristics and wide occurrence in groundwater. However, their specific contribution to nitrification processes has been unclear. The research aimed to unravel the contribution of CMX, AOA, and AOB to nitrification and identify the environmental drivers of their niche differentiation in oligotrophic carbonate rock aquifers.
Article
Ecology
K. Scarlett, S. Denman, D. R. Clark, J. Forster, E. Vanguelova, N. Brown, C. Whitby
Summary: The health of oak trees is influenced by the abundance of ammonia-oxidizing bacteria (AOB) in the soil, with a positive correlation between AOB abundance and soil pH. In contrast, there is no clear relationship between the abundance of archaea (AOA) and tree health. The ratio of soil carbon to nitrogen (C:N) is a key factor influencing denitrifier abundance, with correlations with AOB regardless of tree health.
Article
Immunology
Xu Liu, Guolin He, Yue Lan, Weijie Guo, Xuyuan Liu, Jing Li, Anqing Liu, Miao He, Xinhui Liu, Zhenxin Fan, Yaoyao Zhang
Summary: Studies show that the fetal gut is not sterile and contains a low abundance but metabolically rich microbiome, with Proteobacteria and Actinobacteria as the dominant phyla. The presence of microbes in the fetal gut provides support for the study of early fetal immunity. This study also explores the specific composition of viruses in the fetal gut and the similarities between fetal and adults' gut microbiota, which is valuable for understanding human fetal immunity development during gestation.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Soil Science
Shuikuan Bei, Yinghao Tian, Jun Zhao, Hongyan Zhang, Peter Christie, Xiaolin Li, Zhongjun Jia, Junling Zhang
Summary: Using DNA-SIP technology, the study reveals shifts in active nitrifying bacterial communities in soil under long-term application of different fertilizers (NPK or M) and their temperature sensitivity changes. NPK-amended soil showed the highest labeling of ammonia-oxidizing bacteria, while CK soil had the highest labeling of ammonia-oxidizing archaea. The labeling of nitrite-oxidizing bacteria was lowest in NPK soil and higher at 28°C compared to 35°C regardless of fertilization treatment.
BIOLOGY AND FERTILITY OF SOILS
(2021)
Article
Ecology
Emilie Lyautey, Elodie Billard, Nathalie Tissot, Stephan Jacquet, Isabelle Domaizon
Summary: This study investigated the spatial variability and temporal dynamics of methanogenic Archaea and methanotrophic bacteria in Lake Bourget, France. Changes in both structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics.
Article
Biodiversity Conservation
Muhammad Yasir
Summary: Wastewater contains a diverse microbial community, with bacteria being the predominant type. The effluent exhibited greater diversity in bacterial populations compared to the influent. Metagenomic analysis revealed the presence of various pathogenic/opportunistic bacteria in the domestic sewage samples.
Article
Soil Science
Fuyun Gao, Yaying Li, Haoxin Fan, Jiantao Xue, Huaiying Yao
Summary: In this study, the community structure, abundance, and diversity of comammox Nitrospira in paddy soils were investigated, revealing their wide distribution and high abundance. Environmental factors were found to affect their abundance, and specific amplicon sequence variants (ASVs) had distinct dominant positions in different habitats. These findings provide novel insights into nitrogen cycling and nutrient management in agricultural ecosystems.
Review
Agronomy
Ivan Sazykin, Ludmila Khmelevtsova, Tatiana Azhogina, Marina Sazykina
Summary: The increasing rate of natural resource use leads to an increase in the anthropogenic load on the soil, mainly through industrial, metallurgical, and mining activities, as well as waste and drainage water from various enterprises. The accumulation of heavy metals in the soil negatively affects the soil bacterial community, which is crucial for its health. This review summarizes modern studies on the effect of heavy metals on soil bacterial communities using metagenomic methods and highlights the generally negative impact of pollutants on the taxonomic composition and diversity of bacterial communities, along with factors that modulate metal/metalloid toxicity.
Article
Green & Sustainable Science & Technology
Guiling Ma, Yanting Chen, Pius Ndegwa
Summary: Anaerobic digestion (AD) is a process that extracts renewable bio-methane fuel from biomass substrates, with the structure of the microbiota community closely correlating with methane yield. Firmicutes and Bacteroidetes are significant bacteria in determining methane yield, while Actinobacteria and Proteobacteria are related to decreased yields. Methanosarcina is a major archaeon contributing significantly to methane yield improvements.
RENEWABLE & SUSTAINABLE ENERGY REVIEWS
(2021)
Review
Food Science & Technology
Oluwatobi Esther Ayiti, Olubukola Oluranti Babalola
Summary: This review discusses the role of maize in the industrial revolution, progress toward sustainable production, and the potential of nitrifying bacteria and archaea to achieve sustainable intensification.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2022)
Article
Soil Science
Melanie Armbruster, Tim Goodall, Penny R. Hirsch, Nick Ostle, Jeremy Puissant, Kate C. Fagan, Richard F. Pywell, Robert I. Griffiths
Summary: The study found that land-use intensification can reduce soil carbon stocks and alter microbial community biodiversity and functionality. By surveying unimproved calcareous grasslands and local arable lands, consistent responses of specific microbial taxa to management across geographic scales were identified as key drivers of soil restoration, providing site-independent indicators for calcareous grassland soil function restoration.
EUROPEAN JOURNAL OF SOIL SCIENCE
(2021)
Article
Soil Science
Harry A. Barrat, Jess Evans, David R. Chadwick, Ian M. Clark, Kate Le Cocq, Laura M. Cardenas
Summary: The study identified the significant impact of soil moisture on nitrous oxide emissions, with factors like rewetting degree and water filled pore space playing a crucial role. Substrate availability and fertilizer type were also noted to influence N2O emissions. Future research should focus on investigating how microbial population structure and gene expression profiles change in response to dry/wet cycles.
EUROPEAN JOURNAL OF SOIL SCIENCE
(2021)
Article
Microbiology
Tessa E. Reid, Vanessa N. Kavamura, Maider Abadie, Adriana Torres-Ballesteros, Mark Pawlett, Ian M. Clark, Jim Harris, Tim H. Mauchline
Summary: The research investigated the impact of inorganic chemical fertilizer application on rhizobacterial diversity in wheat, using 16S rRNA gene sequencing and predictive metagenomics. The results showed that fertilization reduced the abundance of potential plant growth-promoting rhizobacteria, suggesting the need for more targeted biofertilization strategies.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Antonio Castellano-Hinojosa, Kate Le Cocq, Alice F. Charteris, Maider Abadie, David R. Chadwick, Ian M. Clark, Jesus Gonzalez-Lopez, Eulogio J. Bedmar, Laura M. Cardenas
Summary: This study investigated the contribution of bacteria and fungi to N2O and CO2 production in soil after nitrate application. The results showed that fungi contributed more to N2O emissions initially, while bacteria had a greater impact later on. The use of antibiotics effectively inhibited the growth of bacteria and fungi, highlighting the importance of considering both microbial groups in greenhouse gas mitigation strategies.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2021)
Review
Soil Science
Na Zhang, Naoise Nunan, Penny R. Hirsch, Bo Sun, Jizhong Zhou, Yuting Liang
Summary: A healthy soil-plant continuum is crucial for sustainable agricultural development and food security. The diversity of soil microorganisms plays a vital role in nutrient cycling, plant growth promotion, and stress alleviation in agroecosystems. Utilizing modern coexistence theory can help in designing and constructing microbial communities for the biological improvement of agroecosystems, particularly in the face of challenges posed by human activities and global climate change.
BIOLOGY AND FERTILITY OF SOILS
(2021)
Article
Microbiology
Andrew L. Neal, David Hughes, Ian M. Clark, Janet K. Jansson, Penny R. Hirsch
Summary: Soil management practices, particularly in agriculture, affect soil microbiomes and their community structures and functional states. Understanding how soil microbiomes respond to combined stresses is crucial for predicting system performance under different land use scenarios and identifying environmentally friendly management practices.
Article
Soil Science
Harry A. Barrat, Alice F. Charteris, Kate Le Cocq, Maider Abadie, Ian M. Clark, David R. Chadwick, Laura Cardenas
Summary: Dry soil when wetted can produce high N2O emissions, but the underlying mechanisms are not solely dependent on substrate concentrations. The study suggests that changes in mRNA abundance related to N cycling genes should be investigated in future studies.
EUROPEAN JOURNAL OF SOIL SCIENCE
(2022)
Article
Microbiology
Heather L. Ruscoe, Rodrigo G. Taketani, Ian M. Clark, George Lund, David Hughes, Ian C. Dodd, Penny R. Hirsch, Tim H. Mauchline
Summary: Land management practices can significantly impact belowground plant traits by altering soil properties. Beneficial Pseudomonas bacteria have the potential to promote plant growth, and this study evaluated the impact of different land management legacies on wheat root associated culturable pseudomonads. The results showed that previous land use can shape the diversity and metabolism of pseudomonad communities near wheat roots.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Soil Science
H. A. Barrat, I. M. Clark, J. Evans, D. R. Chadwick, L. Cardenas
Summary: This study investigated the relationship between drought length, drought intensity, and the size of N2O hot moments. The results showed that drought intensity had a significant impact on hot moments, and drought length followed a quadratic curve, with the largest emissions observed between 10 and 15 days of drought. The study also found that NH4+ was a key factor controlling the emission flux.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Plant Sciences
Maria Oszvald, Kirsty L. Hassall, David Hughes, Adriana Torres-Ballesteros, Ian Clark, Andrew B. Riche, Sigrid Heuer
Summary: This study found genetic diversity in wheat for nitrogen assimilation capacity, with potential for breeding purposes. Wheat varieties were divided into high-GS group with positive response to nitrogen, and inefficient, low-GS group. Future research should focus on nitrogen emissions and reducing N2O emissions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Xiaoxi Li, Jonathan Storkey, Andrew Mead, Ian Shield, Ian Clark, Richard Ostler, Beth Roberts, Achim Dobermann
Summary: Agriculture faces the challenge of meeting competing societal demands to produce food, fiber and fuel while minimizing negative environmental impacts. This necessitates the establishment of long-term agricultural field experiments to study the behavior of different cropping systems. A new experiment has been implemented at Rothamsted to examine the behavior of contrasting cropping systems and initial yield data has been reported.
AGRONOMY FOR SUSTAINABLE DEVELOPMENT
(2023)
Article
Food Science & Technology
Andrew L. Neal, Harry A. Barrat, Aurelie Bacq-Lebreuil, Yuwei Qin, Xiaoxian Zhang, Taro Takahashi, Valentina Rubio, David Hughes, Ian M. Clark, Laura M. Cardenas, Laura-Jayne Gardiner, Ritesh Krishna, Margaret L. Glendining, Karl Ritz, Sacha J. Mooney, John W. Crawford
Summary: Achieving food security requires resilient agricultural systems with improved nutrient-use efficiency, optimized water and nutrient storage in soils, and reduced gaseous emissions. Our study demonstrates how the influence of organic matter on nitrogen transformations in arable soils can be deciphered by integrating metagenomic data with soil structural parameters.
Article
Soil Science
Aurelie Bacq-Labreuil, Andrew L. Neal, John Crawford, Sacha J. Mooney, Elsy Akkari, Xiaoxian Zhang, Ian Clark, Karl Ritz
Summary: Agricultural practices can significantly influence the physical and biological properties of soil, with conversion to grassland leading to notable changes in soil structure over a period of at least a decade post-conversion. Conversion to arable land, on the other hand, did not show a significant impact on soil structural evolution.
EUROPEAN JOURNAL OF SOIL SCIENCE
(2021)
