Article
Environmental Sciences
Shuai Ma, Huanhuan Geng, Changchun Yan, Xiaomin Han, Dan Xu, Furong Zhao, Ruth E. Blake, Beihai Zhou, Huilun Chen, Rongfang Yuan, Baoshi Jin, Haijun Liu, Fei Wang
Summary: The bacterial community in sediments of lakes dominated by macrophytes and lakes without macrophytes show different sensitivities to excessive nutrients. Bacterial communities in macrophyte-dominated areas are more susceptible to changes in nutrient levels and have lower stability compared to macrophyte-free areas.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Microbiology
Megan S. Beaudry, Jincheng Wang, Troy J. Kieran, Jesse Thomas, Natalia J. Bayona-Vasquez, Bei Gao, Alison Devault, Brian Brunelle, Kun Lu, Jia-Sheng Wang, Olin E. Rhodes, Travis C. Glenn
Summary: Environmental microbial diversity is commonly studied using methods such as 16S rRNA gene amplicons and shotgun metagenomics. New 16S rRNA sequence capture baits have been developed to combine the advantages of both methods, providing faster and more cost-effective results for investigating microbial communities. These baits have been shown to increase the proportion of 16S rRNA sequences and reduce analysis time, offering an efficient method for assessing bacterial community composition.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Alan R. Pacheco, Melisa L. Osborne, Daniel Segre
Summary: The study investigates how microbial community properties change with increasing complexity of resource combinations. Results show that environmental composition plays a major role in determining microbiome dynamics, and growth yield may not increase additively with environmental complexity. Factors like species similarity, degree of specialization, and metabolic interactions influence the non-additive behavior of communities in response to combinations of resource pools.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Feilun Wu, Yuanchi Ha, Andrea Weiss, Meidi Wang, Jeffrey Letourneau, Shangying Wang, Nan Luo, Shuquan Huang, Charlotte T. Lee, Lawrence A. David, Lingchong You
Summary: Spatial partitioning modulates the dynamics of microbial communities, promoting the persistence of populations with negative interactions and suppressing those with positive interactions. An intermediate level of partitioning maximizes the overall diversity of the community.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Engineering, Environmental
Mengdie Geng, Weizhen Zhang, Ting Hu, Rong Wang, Xiaoying Cheng, Jianjun Wang
Summary: This study investigated the effects of eutrophication on microbial community structure in shallow lakes in the Yangtze-Huaihe River basin in China. The results showed that eutrophication led to the homogenization of bacterial and fungal communities in both water and sediments. Physicochemical factors such as water temperature, pH, and heavy metals were found to influence the community structure. Importantly, generalist species were found to play a dominant role in explaining the variations in beta diversity along the trophic gradient.
Article
Genetics & Heredity
Alejandro Miguel Cisneros-Martinez, Luis E. Eguiarte, Valeria Souza
Summary: In spring 2016, a shallow hypersaline pond known as Archaean Domes (AD) was discovered in Cuatro Cienegas Basin (CCB). AD has a highly diverse microbial community and a unique viral community structure that remains stable regardless of environmental fluctuations. The diversity of AD is closely related to other CCB sites but forms a cluster of its own.
MICROBIAL GENOMICS
(2023)
Article
Environmental Sciences
Kun Guo, Naicheng Wu, Wei Li, Annette Baattrup-Pedersen, Tenna Riis
Summary: Stream biofilms are complex aggregates of diverse organism groups that are essential for global carbon and nitrogen cycles. The study found that specific phyla dominated the prokaryotic and eukaryotic communities at most sites, with diversity peaking in July and January. Hydrological and physicochemical variables were significant factors in explaining community composition, but a large portion of variation remained unexplained, likely due to unmeasured factors such as light intensity and biological interactions. A multitrophic level perspective is suggested for future biofilm studies to capture the complexity of trophic and non-trophic interactions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemical Research Methods
Philipp Wendering, Zoran Nikoloski
Summary: The composition and functions of microbial communities have significant effects on important traits in various hosts. However, understanding how individual microbe metabolism is influenced by community composition and metabolite leakage is lacking. This study presents a consensus-based approach for improving the quality of draft metabolic reconstructions and proposes a method called COMMIT for gap filling in microbial communities. By applying COMMIT to soil communities, the researchers were able to reduce the gap-filling solution without affecting genomic support. The metabolic interactions identified in the soil communities allowed for the identification of microbes with community roles of helpers and beneficiaries. Therefore, COMMIT offers a versatile and fully automated solution for modeling microbial communities in different biotechnological applications.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Plant Sciences
Takehiro Sasaki, Naohiro I. Ishii, Daichi Makishima, Rui Sutou, Akihito Goto, Yutaka Kawai, Hayami Taniguchi, Kunihiro Okano, Ayumi Matsuo, Alfred Lochner, Simone Cesarz, Yoshihisa Suyama, Kouki Hikosaka, Nico Eisenhauer
Summary: This study provides observational evidence that plant and microbial community composition, rather than diversity, are crucial for sustaining multifunctionality in subalpine moorlands. Furthermore, plant and bacterial beta diversity enhance the dissimilarity of moorland multifunctionality.
JOURNAL OF ECOLOGY
(2022)
Article
Biology
Thomas P. Smith, Shorok Mombrikotb, Emma Ransome, Dimitrios-Georgios Kontopoulos, Samraat Pawar, Thomas Bell
Summary: The response of complex microbial communities to climatic fluctuations is still not well understood. This study investigated how bacterial communities in soil can respond to changes in environmental temperature through a combination of phenotypic plasticity and species sorting. The results showed that distinct communities with different phylogenetic and functional characteristics emerged at different temperatures, with K-strategist taxa favored under cooler conditions and r-strategist taxa favored under warmer conditions. The study also found that the dynamic emergence of distinct communities across a wide range of temperatures is driven by the resuscitation of latent functional diversity.
Article
Engineering, Environmental
Lloyd D. Potts, Alex Douglas, Luis J. Perez Calderon, James A. Anderson, Ursula Witte, James Prosser, Cecile Gubry-Rangin
Summary: Acute environmental perturbations cause changes in microbial community composition and selection of different phylotypes, while chronic perturbations maintain community stability and can lead to the establishment of alternative stable states. This study also demonstrates the functional resilience of ecosystem following environmental perturbations.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Akifumi Nishida, Mayuko Nakagawa, Masayuki Yamamura
Summary: The assembly of microbial communities is influenced by both deterministic and stochastic processes, with large environmental changes leading to a more deterministic microbial community assembly.
Article
Food Science & Technology
Dayun Sun, Junjie Qu, Yu Huang, Jiang Lu, Ling Yin
Summary: Microorganisms in grape skins play important roles in grapevine health, productivity, wine quality, and organoleptic properties. The diversity and composition of microbes in muscadine grape skins were found to be affected by the cultivar, with complex interactions observed among different bacteria and fungi across different cultivars. Predictions of metabolic pathways showed enrichment in carbohydrate, cofactor, amino acid, and other secondary metabolite biosynthesis.
FOOD RESEARCH INTERNATIONAL
(2021)
Article
Microbiology
Shaomin Liu, Jiating Wu, Ziyan Hu, Mengyu Jiang
Summary: This study investigates the effects of different enzymes on sludge hydrolysis efficiency and microbial community. It finds that lysozyme has the best hydrolysis effect and has the greatest impact on effluent quality. The introduction of enzymes has some influence on the microbial diversity of sludge.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Pablo Lechon-Alonso, Tom Clegg, Jacob Cook, Thomas P. Smith, Samraat Pawar
Summary: The study found that in microbial community coalescence events, parent communities that are less competitive and more cooperative contribute more species to the new community due to their superior ability to deplete resources and resist invasions. After repeated coalescence events, communities evolve towards being less competitive and more cooperative, as well as more species-rich, robust, and efficient in resource use.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Engineering, Environmental
Carlos Domingo-Felez, Barth F. Smets
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2020)
Article
Agricultural Engineering
Borja Valverde-Perez, Wei Xing, August A. Zachariae, Monika M. Skadborg, Astrid F. Kjeldgaard, Alejandro Palomo, Barth F. Smets
BIORESOURCE TECHNOLOGY
(2020)
Article
Environmental Sciences
Benyamin Khoshnevisan, Mark Dodds, Panagiotis Tsapekos, Elena Torresi, Barth F. Smets, Irini Angelidaki, Yifeng Zhang, Borja Valverde-Perez
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2020)
Article
Microbiology
Jianxiao Song, Uli Klumper, Leise Riber, Arnaud Dechesne, Barth F. Smets, Soren J. Sorensen, Kristian K. Brandt
FEMS MICROBIOLOGY ECOLOGY
(2020)
Article
Biology
Robert Niederdorfer, Damian Hausherr, Alejandro Palomo, Jing Wei, Paul Magyar, Barth F. Smets, Adriano Joss, Helmut Buergmann
Summary: The research found that anaerobic ammonium oxidizing (anammox) bacteria are highly sensitive to fluctuations in oxygen concentration and temperature under mainstream wastewater treatment conditions, leading to inhibition that affects the efficiency of nitrogen removal. Genomic analysis showed that changes in temperature and oxygen concentration resulted in alterations in gene expression levels within microbial communities, affecting the nitrogen removal process.
COMMUNICATIONS BIOLOGY
(2021)
Review
Engineering, Environmental
Qingxian Su, Anna-Ricarda Schittich, Marlene Mark Jensen, Howyong Ng, Barth F. Smets
Summary: Organic micropollutants (OMPs) can be biotransformed by ammonia-oxidizing bacteria through direct and indirect enzymatic reactions, primarily via hydroxylation and deamination. Ammonia-oxidizing bacteria play a key role in OMP biotransformation during wastewater treatment processes, especially through the activity of the ammonia monooxygenase enzyme.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Engineering, Environmental
Shelesh Agrawal, David G. Weissbrodt, Medini Annavajhala, Marlene Mark Jensen, Jose Maria Carvajal Arroyo, George Wells, Kartik Chandran, Siegfried E. Vlaeminck, Akihiko Terada, Barth F. Smets, Susanne Lackner
Summary: A baseline investigation of qPCR-based analysis for microbial communities in PN/A systems revealed significant variability in DNA extraction and primer efficiency among different laboratories, as well as varying differences in abundance data for different microbial guilds. These insights will provide guidance for interpreting qPCR data for environmental scientists, engineers, and treatment plant operators.
Article
Agricultural Engineering
Jinyu Ye, Huan Gao, Carlos Domingo-F, Junkang Wu, Manjun Zhan, Ran Yu, Barth F. Smets
Summary: Chronic exposure to zinc oxide nanoparticles in a sequencing batch reactor has shown dose-dependent depression effects on ammonia nitrogen and total nitrogen removal efficiencies as well as N2O emissions. The suppressed N2O emissions were positively correlated with the activity ratios of nitrite/NO reductases and N2O reductase.
BIORESOURCE TECHNOLOGY
(2021)
Article
Engineering, Environmental
Liguan Li, Joseph Nesme, Marcos Quintela-Baluja, Sabela Balboa, Syed Hashsham, Maggie R. Williams, Zhuofeng Yu, Soren J. Sorensen, David W. Graham, Jesus L. Romalde, Arnaud Dechesne, Barth F. Smets
Summary: The study of urban wastewater systems in Denmark, Spain, and the UK revealed a significant reduction in antibiotic resistance genes during sewage conveyance, presenting opportunities for antibiotic resistance management and caution for surveillance based on sewage.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Engineering, Environmental
Ling Yuan, Yubo Wang, Lu Zhang, Alejandro Palomo, Jizhong Zhou, Barth F. Smets, Helmut Burgmann, Feng Ju
Summary: A genome-centric quantitative metatranscriptomic approach was used to analyze bacterial hosts of antibiotic resistance genes (ARGs) in urban wastewater treatment plants, revealing widespread presence of ARGs against multiple classes of antibiotics in various bacterial hosts, including potential pathogens and indigenous denitrifying bacteria.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Engineering, Environmental
Toshikazu Suenaga, Takumi Ota, Kohei Oba, Kentaro Usui, Toshiki Sako, Tomoyuki Hori, Shohei Riya, Masaaki Hosomi, Kartik Chandran, Susanne Lackner, Barth F. Smets, Akihiko Terada
Summary: This study investigated the phylogeny of resident N2O-reducing bacteria in an anammox microbial community and quantified individually the processes of N2O production and consumption. The results showed that N2O-reducing bacteria primarily belonged to Burkholderiaceae and Chloroflexus genera, and other less abundant strains in Rhodoferax, Azospirillum, Lautropia, and Bdellovibrio also likely acted as N2O sinks. The study also introduced a novel N-15 tracer method to quantify N2O production and consumption rates, providing insights into the potential N2O-reducing activity in anammox-based processes.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Environmental Sciences
Shaoyi Xu, Wenbo Chai, Rui Xiao, Barth F. Smets, Alejandro Palomo, Huijie Lu
Summary: This study identified Candidatus Nitrospira nitrosa-like comammox bacteria as the predominant ammonia oxidizers in a lab-scale BNR system, with the potential to use acetate and propionate, stimulate ammonia oxidation rate, and interact metabolically with heterotrophs. Comammox bacteria have shown to provide vitamins/cofactors to heterotrophs and receive amino acids in return, contributing to their survival in the system and outcompeting ammonia oxidizing bacteria. Systems with comammox bacteria as the major nitrifiers have great potential for superior performance with low aeration cost and N2O emission at full-scale plants.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Public, Environmental & Occupational Health
Nasreen Hassoun-Kheir, Yoav Stabholz, Jan-Ulrich Kreft, Roberto de la Cruz, Arnaud Dechesne, Barth F. Smets, Jesus L. Romalde, Alberto Lema, Sabela Balboa, Carlos Garcia-Riestra, Eva Torres-Sangiao, Ami Neuberger, David Graham, Marcos Quintela-Baluja, Dov J. Stekel, Jay Graham, Amy Pruden, Joseph Nesme, Soren Johannes Sorensen, Rupert Hough, Mical Paul
Summary: By utilizing a systematic review and Delphi consensus method, the EMBRACE-WATERS statement was developed as a checklist of recommendations for reporting studies of AMR in wastewater and related aquatic environments. The consensus among a multidisciplinary panel of experts resulted in 21 items comprising essential elements for high-quality reporting, with explanations and reporting examples provided for each item. The statement aims to improve reporting quality, facilitate communication among researchers, and guide peer-reviewers and editors in evaluating manuscripts in the field of AMR research in aquatic environments.
Article
Biochemistry & Molecular Biology
Arda Gulay, Greg Fournier, Barth F. Smets, Peter R. Girguis
Summary: Many aerobic microbes can use alternative electron acceptors under oxygen-limited conditions, through extracellular electron transfer (EET) to oxidants like iron oxide and manganese oxide. Nitrosomonas communis, an aerobic ammonia-oxidizer, was found to be able to utilize a poised electrode to maintain metabolic activity in anoxic conditions, indicating a potential for EET. The presence of multiheme cytochromes further suggests this capacity. Molecular clock analysis and phylogenetic reconciliations show that the evolution of EET in beta-proteobacterial ammonia oxidizers and the acquisition of multiheme c-type EET proteins likely occurred during the Proterozoic era.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Agricultural Engineering
Sike Wang, Kento Ishii, Heng Yu, Xuchuan Shi, Barth F. Smets, Alejandro Palomo, Jiane Zuo
Summary: The study found that rapid temperature drops had impacts on the performance of the anammox process and the metabolism of core microbial populations, with the metabolism of AnAOB responding more significantly to low temperatures compared to heterotrophs.
BIORESOURCE TECHNOLOGY
(2021)
