Article
Environmental Sciences
Ademir Sergio Ferreira Araujo, Ana Roberta Lima Miranda, Arthur Prudencio de Araujo Pereira, Wanderley Jose de Melo, Vania Maria Maciel Melo, Sabrina Hermelindo Ventura, Eudemio Sousa Brito Jr, Erika Valente de Medeiros, Fabio Fernando Araujo, Lucas William Mendes
Summary: This study assessed the microbial community in the rhizosphere of maize and cowpea grown in Cr-contaminated soils using amplicon sequencing. The results showed that the microbial community in the maize rhizosphere clustered together, while the microbial community in the cowpea rhizosphere did not present clear clustering. Furthermore, Cr contamination had different effects on specific bacterial groups in the rhizospheres of maize and cowpea.
Review
Microbiology
Diego J. Castillo, Choaro D. Dithugoe, Oliver K. Bezuidt, Thulani P. Makhalanyane
Summary: This study examines the microbial diversity and functionality in the Southern Ocean (SO), emphasizing the relationships between microbial communities and other trophic levels. The seasonal variations and characteristic features of the SO influence community composition and ecosystem functions. The study highlights the importance of abundant bacteria in recycling organic matter and discusses the effects of climate change on marine microbiota in the SO.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Article
Microbiology
Alexis M. Walker, Mary Beth Leigh, Sarah L. Mincks
Summary: The study analyzed the structure and composition of benthic microbial communities in the North American Arctic, identifying four main prokaryotic assemblages affected by environmental conditions and organic matter input. The results suggest that environmental correlates and distribution of sediments are influenced by water depth and geographical factors.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Ecology
Christina Birnbaum, Jennifer Wood, Erik Lilleskov, Louis James Lamit, James Shannon, Matthew Brewer, Samantha Grover
Summary: The structure and function of microbial communities in peatlands are influenced by soil abiotic factors, and peatland degradation reduces microbial richness and alters microbial functions.
Article
Soil Science
Stafva Lindstrom, Sari S. Timonen, Liselotte Sundstrom
Summary: In this study, the bacterial and fungal microbiomes of the ant Formica exsecta were investigated, finding that the microbial communities inside the ants differ from those in their nest material. The bacterial species diversity, species richness, ? diversity, evenness, and fungal species richness were found to be lower in ants compared to the nest material. The fungal communities in the ants were also found to be less stable than the bacterial ones.
EUROPEAN JOURNAL OF SOIL SCIENCE
(2023)
Article
Ecology
N. V. Patin, Z. A. Dietrich, A. Stancil, M. Quinan, J. S. Beckler, E. R. Hall, J. Culter, C. G. Smith, M. Taillefert, F. J. Stewart
Summary: Exploration of oxygen-depleted marine environments has led to the discovery of novel microbial taxa and metabolic capabilities, expanding our understanding of microbial evolution and ecology. The study of Amberjack Hole on the Florida continental shelf revealed stable microbial communities with extensive biochemical capabilities for sulfur and nitrogen cycling. Overall, the blue hole habitat provides a natural marine laboratory for sampling taxa with potentially important roles in redox-stratified microbial processes.
Article
Environmental Sciences
K. L. Korbel, P. Greenfield, G. C. Hose
Summary: This study examines the impact of different land uses (irrigated and non-irrigated) on groundwater microbial communities. The results show that irrigated land uses significantly affect microbial community structure and diversity within groundwaters, with lower microbial diversity in irrigated sites. Differences in community structure and function were observed between catchments and land uses, with irrigated sites having higher abundances of microbes with nitrifying capabilities. Specific taxonomic groups may be useful indicators of long-term nitrogen contamination in groundwaters.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemical Research Methods
Yulia Fridman, Zihan Wang, Sergei Maslov, Akshit Goyal
Summary: Recent observations have shown that closely related strains of the same microbial species can stably coexist in different environments. A consumer-resource model of microbial ecosystems suggests that differentiation of strains based on their growth rates in high and low nutrient conditions enables coexistence. The model also demonstrates that between 1 and 3 strains of a species typically coexist, consistent with experimental observations.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Environmental Sciences
Elena Piano, Federico Biagioli, Giuseppe Nicolosi, Claudia Coleine, Anna Poli, Valeria Prigione, Andrea Zanellati, Rosangela Addesso, Giovanna Cristina Varese, Laura Selbmann, Marco Isaia
Summary: Anthropogenic disturbance on natural ecosystems is increasing, affecting all components of the ecosystems. A metacommunity framework is needed to understand the response of different biocoenosis types to human disturbance. Through advanced molecular techniques, sediment communities of Fungi, Bacteria, and Archaea in Italian show caves were investigated to unravel the effects of tourism on their diversity and identify changes in the driving forces of community composition. The study showed that cave tourism directly affects the community of Bacteria and indirectly influences Fungi and Archaea.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Ecology
Daniel A. Nielsen, Noah Fierer, Jemma L. Geoghegan, Michael R. Gillings, Vadim Gumerov, Joshua S. Madin, Lisa Moore, Ian T. Paulsen, T. B. K. Reddy, Sasha G. Tetu, Mark Westoby
Summary: The relationship between genome size and traits in bacteria and archaea has been quantified, revealing that aerobic species have genomes about 35% larger than anaerobic species, with a similar mix of gene functions. Larger genomes allow for more versatility in metabolizing substrates and responding to different environments, indicating that aerobic habitats may present more dynamic challenges and opportunities compared to anaerobic habitats.
Article
Environmental Sciences
Zala Schmautz, Jean-Claude Walser, Carlos A. Espinal, Florentina Gartmann, Ben Scott, Joel F. Pothier, Emmanuel Frossard, Ranka Junge, Theo H. M. Smits
Summary: Aquaponics systems have unique microbial communities in different compartments, with nitrifying bacteria identified in the hydroponic compartments. The composition of microbial communities varied over time in the anaerobic compartment, with more archaeal reads obtained from sludge samples. Fresh fish feces had lower bacterial diversity with a discrete gut flora composition. The most pronounced differences in microbial community compositions were observed between the aerobic and anaerobic loops of the system.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Gwendoline M. David, Purificacion Lopez-Garcia, David Moreira, Benjamin Alric, Philippe Deschamps, Paola Bertolino, Gwendal Restoux, Emma Rochelle-Newall, Elisa Thebault, Marianne Simon, Ludwig Jardillier
Summary: Microbial communities in small freshwater ecosystems are mainly driven by environmental conditions, showing diversity and uniqueness in composition and structure. Despite geographical proximity, microbial communities in different ecosystems exhibit marked differences, with seasonal patterns observed in archaea, bacteria, and microbial eukaryotes. Interannual community assembly is influenced by biotic associations despite relatively stable environmental parameters over a 2-year period.
Article
Ecology
Tatyana Zamkovaya, Jamie S. Foster, Valerie de Crecy-Lagard, Ana Conesa
Summary: Microbial dark matter, consisting of unknown microbes, plays essential ecological roles and occupies top hubs within their communities. Excluding unknown taxa results in a reduction in network centrality measures, highlighting the importance of these unknown organisms.
Article
Veterinary Sciences
Eslam Ahmed, Rintaro Yano, Miho Fujimori, Deepashree Kand, Masaaki Hanada, Takehiro Nishida, Naoki Fukuma
Summary: The study found that Mootral can increase the production of total volatile fatty acids and propionate in a dose-dependent manner, while reducing the proportion of acetate and acetate/propionate ratio. Additionally, Mootral significantly decreased methane production, while minimal effects were observed on pH, digestibility, and ammonia-nitrogen.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Microbiology
Amanda Goncalves Bendia, Leandro Nascimento Lemos, Lucas William Mendes, Camila Negrao Signori, Brendan J. M. Bohannan, Vivian Helena Pellizari
Summary: Active volcanoes in Antarctica have remarkable temperature and geochemical gradients that could select for a wide variety of microbial adaptive mechanisms and metabolic pathways. Microbial communities from different temperature environments showed distinct metabolic potentials and survival strategies, reflecting their adaptability to extreme conditions.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biology
George Westmeijer, Maliheh Mehrshad, Stephanie Turner, Linda Alakangas, Varvara Sachpazidou, Carina Bunse, Jarone Pinhassi, Marcelo Ketzer, Mats Astrom, Stefan Bertilsson, Mark Dopson
Summary: This study found that the microbial communities in deep biosphere groundwaters are mainly comprised of autochthonous species, rather than migratory surface representatives.
COMMUNICATIONS BIOLOGY
(2022)
Editorial Material
Cell Biology
Lucie Delemotte, Sarahi L. Garcia, Alejandro Rodriguez-Gijon, Erdinc Sezgin, Anniina Vihervaara
JOURNAL OF CELL SCIENCE
(2022)
Article
Multidisciplinary Sciences
Roohollah Kheiri, Maliheh Mehrshad, Ahmad Ali Pourbabaee, Antonio Ventosa, Mohammad Ali Amoozegar
Summary: Lake Urmia in Iran is a hypersaline environment with a salinity of about 27%. Metagenomic analysis revealed that the microbial community in the lake is dominated by Haloferacaceae family (69.8%), mainly Haloquadratum (59.3%) and Halonotius (9.1%). The bacterial community is mainly composed of Salinibacter ruber (23.3%). Genomic variation analysis showed a high level of SNVs and insertions in Lake Urmia's community, possibly due to transformation caused by the extreme conditions and high ionic concentrations.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Vinicius S. S. Kavagutti, Paul-Adrian Bulzu, Cecilia M. M. Chiriac, Michaela M. M. Salcher, Indranil Mukherjee, Tanja Shabarova, Vesna Grujcic, Maliheh Mehrshad, Vojtech Kasalicky, Adrian-Stefan Andrei, Jitka Jezberova, Jaromir Seda, Pavel Rychtecky, Petr Znachor, Karel Simek, Rohit Ghai
Summary: This study performed high-resolution sampling of the spring bloom in a freshwater reservoir and identified previously unknown microbial taxa using metagenome-assembled genomes. The recovered genomes provide insights into the distributional dynamics and doubling times of microbial lineages during the bloom. Additionally, the study uncovered the presence of aplastidic cryptophytes and giant viruses, offering new understanding of plankton dynamics.
Correction
Multidisciplinary Sciences
Roohollah Kheiri, Maliheh Mehrshad, Ahmad Ali Pourbabaee, Antonio Ventosa, Mohammad Ali Amoozegar
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Krzysztof T. Jurdzinski, Maliheh Mehrshad, Luis Fernando Delgado, Ziling Deng, Stefan Bertilsson, Anders F. Andersson
Summary: The crossing of environmental barriers poses adaptive challenges and bacterial communities in freshwater-marine transitions are rarely related to brackish counterparts. This study conducted a phylogenomic analysis of metagenome-assembled genomes to investigate the molecular adaptations facilitating cross-biome transitions. The results showed that cross-biome transitions were rare, ancient, and mostly directed toward the brackish biome, accompanied by systematic changes in proteomes and gene functions.
Article
Zoology
D. Fontaneto, E. Sottoriva, A. Rodriguez-Gijon, D. Bedulina, A. Gurkov, O. A. Timoshkin, V. N. Ivanenko
Summary: An extreme radiation of species occurred in Lake Baikal, Russia, resulting in about 350 endemic species of amphipods. This study aims to investigate the coevolution and species-specific associations between bdelloid rotifers and amphipods in Lake Baikal. We found that only one bdelloid species, Embata parasitica, lives associated with multiple amphipod species belonging to different families, suggesting the possibility of cryptic species. In addition, nine bdelloid species were discovered, increasing the known diversity of bdelloid rotifers in the area to 12 species.
EUROPEAN ZOOLOGICAL JOURNAL
(2023)
Article
Ecology
Carlotta Meriggi, Maliheh Mehrshad, Richard K. Johnson, Ane T. Laugen, Stina Drakare
Summary: Species distribution models calibrated with bioclimatic variables suggest a high probability of range expansion of the invasive toxin producing cyanobacterium Raphidiopsis raciborskii to Sweden. However, field-based surveys and in-silico screening did not fully support this prediction, indicating the need for proactive monitoring with high temporal and spatial frequency. The inconsistencies between the models and monitoring approaches highlight the uncertainties in solely focusing on climate drivers and the potential limitations of early invasion detection.
ISME COMMUNICATIONS
(2023)
Article
Ecology
Alejandro Rodriguez-Gijon, Moritz Buck, Anders F. F. Andersson, Dandan Izabel-Shen, Francisco J. A. Nascimento, Sarahi L. L. Garcia
Summary: This study investigates the ecological implications of microbial genome size variation in benthic and pelagic habitats of the Baltic Sea. It finds that genome size is associated with depth and salinity, with benthic genomes being larger than pelagic genomes. Additionally, the study shows differences in functions, metabolic potential, and taxonomy between Bacteria inhabiting sediment and water column.
ISME COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Moritz Buck, Maliheh Mehrshad, Stefan Bertilsson
Summary: Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades. mOTUpan is a novel method for computing the core genome of highly diverse genome sets. The core-genome prediction of mOTUpan is computationally efficient and can be applied to genomes with lower completeness thresholds.
NAR GENOMICS AND BIOINFORMATICS
(2022)