Article
Microbiology
Joanna Tannous, Casey M. Cosetta, Milton T. Drott, Tomas A. Rush, Paul E. Abraham, Richard J. Giannone, Nancy P. Keller, Benjamin E. Wolfe
Summary: Using an antibacterial Penicillium isolate and a cheese rind microbial community, this study demonstrates that a fungal specialized metabolite can regulate the diversity of bacterial communities. It reveals the role of global regulators in controlling bacterial community assembly and highlights the ecological function of fungal specialized metabolites.
Article
Environmental Sciences
Qingxin Meng, Shuang Liu, Yue Guo, Yunlong Hu, Zhidan Yu, Ayodeji Bello, Zhigang Wang, Weihui Xu, Xiuhong Xu
Summary: This study used co-occurrence network analysis to explore the interspecific relationships within and between bacterial and fungal communities during composting of cow manure. The findings showed that the interactions within bacterial communities were tighter and more responsive to environmental changes, while the fungal network had a better buffer capacity. The detection of keystone taxa validated the connectivity of modules and networks.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Microbiology
Nana Wei, Jinmiao Lu, Yi Dong, Shibo Li
Summary: This study investigated the microbial community and antibiotic resistome in wild tick species. The results showed that the microbial composition is variable, with Proteobacteria and Bacteroidetes being the dominant phyla. A total of 100 different antibiotic resistance genes (ARGs) across 12 antibiotic classes were identified, with aminoglycosides, multidrug, macrolide-clinolamide-streptogramin B, and tetracycline resistance genes being the most dominant. Network analysis revealed potential host genera for different ARGs. This study provides a comprehensive overview of the diversity and abundance of ARGs in wild ticks, highlighting their potential role as disseminators of ARGs into the environment and vertebrate hosts.
Article
Microbiology
Wangkai Fang, Tingyu Fan, Liangji Xu, Shun Wang, Xingming Wang, Akang Lu, Yongchun Chen
Summary: Coal mining subsidence lakes are characterized by clear season heterogeneity of bacterial communities, with higher alpha-diversity and functional diversity in summer driven by temperature and chlorophyll-a. While winter communities are influenced by deterministic processes, summer communities are dominated by stochastic processes, forming a highly complex and stable community structure. These findings provide new insights into the effects of seasonal succession on microbial assembly processes in coal mining subsidence lake ecosystems.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Environmental Sciences
Li Duan, Jia Jia-Li, Ling-Zi Yin, Xiao-Qing Luo, Manzoor Ahmad, Bao-Zhu Fang, Shan-Hui Li, Qi-Qi Deng, Pandeng Wang, Wen-Jun Li
Summary: This study collected water and sediment samples from the Pearl River Estuary to investigate the microbial diversity, community structures, network properties, and potential keystone taxa in estuarine ecosystems. The sediment microbial community was found to be more diverse but less complex in terms of network properties compared to particle-attached and free-living communities. The composition of the communities was influenced by different environmental factors in each habitat. There were taxonomically divergent keystone taxa among the community networks in three habitats. Overall, the study provided detailed information on estuarine microbial communities and their potential keystone species, which can help evaluate the impact of anthropogenic disturbances and facilitate microbial-based environmental monitoring.
ENVIRONMENTAL RESEARCH
(2022)
Article
Environmental Sciences
Xiaowen Yu, Xueyu Gao, Li Shang, Xiaoyu Wang, Yutian Jiao, Xiao-Hua Zhang, Xiaochong Shi
Summary: This study investigates the impact of seasonal and spatial heterogeneity in the epipelagic seawater of the Nordic Sea on microbial community structure. By collecting 54 seawater samples from different locations in the Nordic Sea, the study reveals the existence of spatiotemporal patterns of microbial communities and the influence of ocean currents on community assembly processes. The results show significant differences between bacterial groups in different seasons and ocean currents, suggesting the importance of considering these factors in understanding microbial community dynamics in the Nordic Sea.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Agricultural Engineering
Lucia Blasco, Minna Kahala, Satu Ervasti, Elina Tampio
Summary: This study investigated the effects of co-feedstock changes on the performance and evolution of microbial consortia in anaerobic digestion of cow slurry. Despite drastic changes in co-feedstock composition, stable and flexible anaerobic digestion can be achieved with cautious operation of the process.
BIORESOURCE TECHNOLOGY
(2022)
Article
Environmental Sciences
Chinedu C. Obieze, Gowher A. Wani, Manzoor A. Shah, Zafar A. Reshi, Andre M. Comeau, Damase P. Khasa
Summary: Freshwater lakes are crucial reservoirs and drinking water sources globally. However, anthropogenic activities have introduced nutrients, heavy metals, and toxic chemicals, which threaten the microbiota that support these ecosystems. This study examines the impact of human activities on bacterial community diversity, assembly mechanisms, and co-occurrence patterns in freshwater lakes in Canada and India. The findings demonstrate that lake water chemistry and geographic distance play a role in altering bacterial diversity and composition. Anthropogenic activities heavily influence species distribution, with dispersal limitation, homogenous selection, and drift as the main assembly mechanisms.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Geosciences, Multidisciplinary
Ying Wang, Liguo Dong, Min Zhang, Yongxing Cui, Xiaoxiong Bai, Bin Song, Jiawen Zhang, Xuan Yu
Summary: During plantation development, the microbial community structures in different soil compartments were influenced by changes in soil properties and stand age, and the assembly mechanisms of soil microbial communities were mainly governed by dispersal limitation. The keystone species in the rhizosphere played important roles in soil nitrogen and phosphorus cycling. The complexity of bacterial networks increased along the plantation chronosequence, while fungal network complexity showed no clear age-related trend but was higher in the rhizosphere than bulk soils.
Article
Oceanography
Wentao Zhu, Xiangbo Liu, Ming Zhu, Jingquan Xia, Rouwen Chen, Xiubao Li
Summary: The study found that summer upwelling areas could provide a thermal refuge for coral reefs under climate change. The research focused on the environmental adaptation of scleractinian coral to upwelling environments, comparing coral holobionts in the Qiongdong upwelling and non-upwelling regions. It was observed that corals in the upwelling environment had higher Symbiodiniaceae density, tissue biomass, and protein content compared to those in non-upwelling environments. Furthermore, the coastal upwelling under human influence significantly shaped coral bacterial communities and decreased their diversity.
JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS
(2023)
Article
Environmental Sciences
Li Ji, Benjawan Tanunchai, Sara Fareed Mohamed Wahdan, Martin Schaedler, Witoon Purahong
Summary: The research found that under future climate conditions, the complexity and modularity of plastic-associated microbial networks increased, with more competition and cooperation between bacteria and fungi. Drift was the main factor influencing the assembly of bacterial and fungal communities.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Engineering, Environmental
Lijie Zhou, Yongzhou Lai, Zhiyuan Shao, Yixin Jian, Wei-Qin Zhuang
Summary: Keystone bacteria associated with thiosulfate-driven autotrophic denitrification were identified in this study. Five anoxic bioreactors with varying S/N ratios were fed with synthetic wastewater containing nitrate. The dominant phyla in the bioreactors were Proteobacteria, Bacteriodetes, and Firmicutes, while Thiobacillus, Pseudomonas, Arenimonas, and Thauera were the predominant genera. Thiobacillus and Thauera were found to have the complete nitrate reduction pathway and were essential for thiosulfate oxidation. However, their collaboration might have resulted in extracellular electron transportation and low electron utilization in the autotrophic denitrification process.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Xiaowei Ding, Kaihui Liu, Qingyun Yan, Xingyu Liu, Ni Chen, Guoliang Wang, Shuai He
Summary: Metabolites in root-associated soils play a significant role in shaping the diversity and assembly of diazotrophic communities, with sugars and organic acids being key factors. The concentration of these metabolites influences the composition of diazotrophic taxa, which can vary across different land types and plant species. Additionally, deterministic ecological processes and the presence of specific organic acids like 3-(4-hydroxyphenyl)propionic acid and citric acid are important predictors of diazotrophic community characteristics in desert habitats on the Tibetan Plateau.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Engineering, Environmental
Jericho Victor Mercado, Mitsuhiko Koyama, Kiyohiko Nakasaki
Summary: Fluctuations in the organic loading rate (OLR) of anaerobic digestion (AD) can lead to unstable methane production. This study investigated the impact of repeated high OLR shocks on the microbial community dynamics within AD. The results showed that less frequent organic load shocks led to a decrease in methane productivity and a breakdown of the microbiome network structure. The identification of influential species in the network structure revealed the importance of Anaerovorax, Spirochaetales, and Synergistales. It was inferred that the OLR shocks shifted the microbiome activity away from methane production pathways. Overall, developing a resilient AD microbiome would be necessary for small-scale AD systems that can withstand infrequent organic loading shocks.
Article
Engineering, Environmental
Jericho Victor Mercado, Mitsuhiko Koyama, Kiyohiko Nakasaki
Summary: This study explores the relationship between AD performance and dynamics of microbial interactions in response to high OLR shocks at different frequencies, finding that less frequent organic load shocks lead to deterioration of methane productivity and breakdown of the microbiome network structure. Identification of key species influencing the network structure implies that the impact imposed by OLR shocks shifts microbiome activity towards pathways not contributing to methane production. Establishing a small-scale AD system resilient to infrequent organic loading shocks is key for managing OLR fluctuations.
Article
Biotechnology & Applied Microbiology
E. Emilia Rios-Del Toro, Edgardo I. Valenzuela, Nguyen E. Lopez-Lozano, M. Guadalupe Cortes-Martinez, Miguel A. Sanchez-Rodriguez, Omar Calvario-Martinez, Salvador Sanchez-Carrillo, Francisco J. Cervantes
Article
Environmental Sciences
Erika E. Rios-Valenciana, Roberto Briones-Gallardo, Luis F. Chazaro-Ruiz, Nguyen E. Lopez-Lozano, Reyes Sierra-Alvarez, Lourdes B. Celis
Article
Plant Sciences
Ernesto Mascot-Gomez, Joel Flores, Nguyen E. Lopez-Lozano, Laura Yanez-Espinosa
Article
Microbiology
Edgardo I. Valenzuela, Claudia Padilla-Loma, Nicolas Gomez-Hernandez, Nguyen E. Lopez-Lozano, Sergio Casas-Flores, Francisco J. Cervantes
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Nohemi G. Campos-Quevedo, Irene Sanchez-Andrea, Nguyen E. Lopez-Lozano, Alfons J. M. Stams, Lourdes B. Celis
Summary: From sediment enrichments from a natural acidic source, seven sulfate-reducing consortia were developed, capable of consuming acetate at acidic pHs. These consortia used 53-75% of reducing equivalents for sulfate reduction and showed slightly higher sulfide production rates at acidic conditions. The microbial diversity of the consortia was dominated by acetotrophic sulfate reducers and fermenting bacteria.
JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY
(2021)
Article
Ecology
Ernesto Mascot-Gomez, Joel Flores, Nguyen E. Lopez-Lozano
Summary: This study investigated the diversity of seed-associated microbiome in cactus and found a high richness of microbial communities with potential pathogens and beneficial microorganisms, which could influence the germination percentage and seedling's development. Notable bacterial groups include Kluyvera, Bacillus, Paenibacillus, and Stenotrophomonas; for fungi, classes Tremellomycetes, Dothideomycetes, Eurotiomycetes, Leotiomycetes, and Sordariomycetes were highlighted.
JOURNAL OF ARID ENVIRONMENTS
(2021)
Article
Ecology
Guadalupe Medina-de La Rosa, Felipe Garcia-Oliva, Cesare Ovando-Vazquez, Lourdes B. Celis-Garcia, Lucia Lopez-Reyes, Nguyen Esmeralda Lopez-Lozano
Summary: This study investigates how the changes in amino acids in the rhizosphere of Agave lechuguilla affect the composition, functions, and activity of beneficial rhizobacteria. The most abundant genera in the rhizobacterial community were found to be from the phylum Proteobacteria and Bacteroidetes. Bacillus, representing Firmicutes, was mainly present in the phosphorus-mineralizing bacteria community, indicating its distribution and versatility in harsh desert environments. Additionally, a high proportion of unknown taxa of nitrogen-fixing bacteria was discovered, suggesting the presence of unexplored diversity in the rhizosphere of these plants.
Article
Ecology
Rosaura G. Alfaro G. Garcia, David Douterlungne, Nguyen E. Lopez E. Lozano, Elisabeth Huber-Sannwald, Felipe Garcia-Oliva
Summary: Deforestation and forest degradation are ongoing at alarming rates, and ecological restoration efforts often focus on aboveground processes while neglecting belowground processes. This study examined the abundance and activity of nutrient improvement bacteria in the rhizosphere of Quercus mexicana plantlets in a disturbed oak forest in central Mexico, comparing different restoration interventions and land-use legacies. The results showed that restoration interventions had varying effects on soil functioning across different landscape patches, with an increase in P-mineralizing bacteria abundance and activity in eroded landslide and pastureland, and an increase in N-fixing bacteria only in the landslide site with low organic matter content. Surprisingly, enhancing bacterial activity and abundance did not necessarily improve short-term seedling performance. The study highlights the importance of considering landscape heterogeneity and matching restoration interventions with specific degradation factors in each landscape patch, as well as the need to monitor soil health for a comprehensive understanding of restoration trajectories.
RESTORATION ECOLOGY
(2023)
Article
Agronomy
Angel J. Estrada-Gonzalez, Guadalupe Medina-De la Rosa, Elihu Bautista, Joel Flores, Nguyen E. Lopez-Lozano
Summary: Mexican cactus Echinocactus platyacanthus alters its physiology in response to environmental changes, leading to changes in the rhizosphere bacterial community. Under dry conditions, the cactus increases chlorophyll b and carotenoids to adapt to limited water and nutrient availability. This physiological regulation cascade also affects the profile of amino acids released by its roots, resulting in changes in the abundance of beneficial bacteria.
Article
Ecology
Guadalupe Medina-de la Rosa, Felipe Garcia-Oliva, Nguyen Esmeralda Lopez-Lozano
Summary: Root exudates contain sugars, organic acids, and amino acids, which attract beneficial bacteria in the rhizosphere. However, the composition of root exudates in arid plants like Agave lechuguilla Torr is largely unknown. This study examined the effect of different metabolites from A. lechuguilla Torr on enzymatic activity, abundance of nitrogen-fixing and organic phosphorus mineralizing bacteria, and nutrient availability in the soil. The results showed that amino acids increased nitrogenase and phosphatase activity, leading to changes in nutrient concentration in the soil. This work highlights the importance of bacteria in nutrient recycling and offers insights for plant establishment in harsh environments.
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2023)
Article
Microbiology
Guadalupe Medina-de la Rosa, Felipe Garcia-Oliva, Angel G. Alpuche-Solis, Cesare Ovando-Vazquez, Nguyen E. Lopez-Lozano
Summary: This study shows that mature lechuguilla plants stimulate the activity and abundance of nutrient-improvement rhizobacteria in the Chihuahuan Desert. Nutrient availability plays a crucial role in shaping the structure of bacterial communities. Hub genera in the bacterial community are associated with nutrient availability mechanisms.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Dentistry, Oral Surgery & Medicine
Enid Karina Salas-Lopez, Sergio Casas-Flores, Nguyen Esmeralda Lopez-Lozano, Esther Layseca-Espinosa, Christian A. Garcia-Sepulveda, Perla del Carmen Nino-Moreno, Amaury Pozos-Guillen
MEDICINA ORAL PATOLOGIA ORAL Y CIRUGIA BUCAL
(2020)
Article
Agronomy
Margarita Maria Sarria Carabali, Felipe Garcia-Oliva, Luis Enrique Cortes Paez, Nguyen E. Lopez Lozano
Article
Agronomy
Margarita Maria Sarria Carabali, Felipe Garcia-Oliva, Luis Enrique Cortes Paez, Nguyen E. Lopez-Lozano