Article
Ecology
Nathan G. King, Roberto Uribe, Pippa J. Moore, Hannah S. Earp, Adam Gouraguine, Diego Hinostroza, Alejandro Perez-Matus, Kathryn Smith, Dan A. Smale
Summary: Ecological communities are influenced by processes operating at different spatial scales. Our understanding of microbial biodiversity patterns lags behind that of macro-communities. Bacteria, whether as free-living or associated with host eukaryotes, play important roles in host performance and ecosystem functioning.
Article
Ecology
Ademir Sergio Ferreira Araujo, Arthur Prudencio de Araujo Pereira, Vania Maria Maciel Melo, Erika Valente de Medeiros, Lucas William Mendes
Summary: Soils from the semiarid regions of Brazil are at high risk of desertification due to various factors. However, restoration strategies such as conservationist practices and grazing exclusion have shown potential in recovering the richness and diversity of soil bacterial and archaeal communities. These strategies also improve the connectivity and functionality of soil microorganisms over time.
Article
Microbiology
Kayla M. Williamson, Brandie D. Wagner, Charles E. Robertson, Mark J. Stevens, Marci K. Sontag, Peter M. Mourani, J. Kirk Harris
Summary: The study aimed to increase the sensitivity of bacterial community analysis without impacting community composition or interfering with cluster formation during sequencing. The modified PCR protocol showed increased sensitivity in detecting bacterial communities in airway samples, crucial for studying the highly variable human airway microbiome.
Article
Environmental Sciences
R. G. Bulgarelli, M. F. A. Leite, M. De Hollander, P. Mazzafera, S. A. L. Andrade, E. E. Kuramae
Summary: The availability of soil phosphorus can affect plant growth, root-soil interactions, and rhizosphere microbial community composition. This study investigated the rhizosphere microbial communities of 24 species of eucalypts under low or sufficient soil phosphorus availability. It was found that eucalypt species identity was the main factor determining the composition of the rhizosphere microbial community, while the effect of phosphorus availability varied among species.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Camille Prioux, Romie Tignat-Perrier, Ophelie Gervais, Tristan Estaque, Quentin Schull, Stephanie Reynaud, Eric Beraud, Bastien Merigot, Anais Beauvieux, Maria-Isabelle Marcus, Justine Richaume, Olivier Bianchimani, Adrien Cheminee, Denis Allemand, Christine Ferrier-Pages
Summary: This study investigates the role of bacteria in tissue loss of octocoral species caused by heatwaves. The results indicate that the main bacterial symbionts do not directly cause tissue loss, but opportunistic and pathogenic bacteria proliferate instead. The study highlights the importance of considering both relative and absolute quantification approaches in evaluating the impact of stressors on coral microbiome, and provides insights into the ecological implications of heatwaves on marine animal forests.
Article
Plant Sciences
Carmen Haro, Manuel Anguita-Maeso, Madis Metsis, Juan A. Navas-Cortes, Blanca B. Landa
Summary: The study assessed the impact of different DNA extraction kits and primer pairs on bacterial community assessment in olive xylem sap, indicating that the choice of extraction method significantly influences the results.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Ecology
Vijaya Raghavan Rangamaran, Sai H. Sankara Subramanian, Karpaga Raja Sundari Balachandran, Dharani Gopal
Summary: This study investigated the bacterial communities at different depths of the Arabian Sea OMZ using high-throughput sequencing. The results showed high bacterial diversity in deep waters and sediment samples, with less richness at the core OMZ depths. Bacterial community composition varied with depth and dissolved oxygen levels, and predictive functional annotation suggested the presence of active nitrogen, sulphur, carbon, and methane metabolic cycles. The study also revealed the presence of nitrogen reduction bacterial group below the core OMZ depths, which may provide insights into the expansion of OMZ region in Arabian Sea.
Article
Microbiology
Marcelle Muniz Barreto, Maren Ziegler, Alexander Venn, Eric Tambutte, Didier Zoccola, Sylvie Tambutte, Denis Allemand, Chakkiath Paul Antony, Christian R. Voolstra, Manuel Aranda
Summary: Ocean warming and acidification, direct consequences of climate change, affect coral reefs worldwide. This study found that ocean acidification has stronger effects on the active microbial community associated with corals, compared to the resident community. The results suggest that rDNA- and rRNA-based sequencing are complementary tools for investigating the effects of environmental change on microbial assemblage structure and activity.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Ecology
Kathryn Lee Morrissey, Ljiljana Ivesa, Soria Delva, Sofie D'Hondt, Anne Willems, Olivier De Clerck
Summary: Algal-associated bacteria play a crucial role in the ecological success of marine green macroalgae, exhibiting resistance and resilience to environmental stress. Bacterial communities vary in composition among different algal niches, leading to unique responses to environmental perturbations. Nutrient enrichment significantly influences epimicrobiota, while temperature and nutrient stress impact rhizomicrobiota, with the lowest overall resistance observed.
ECOLOGY AND EVOLUTION
(2021)
Article
Oncology
Massimiliano Mutignani, Roberto Penagini, Giorgio Gargari, Simone Guglielmetti, Marcello Cintolo, Aldo Airoldi, Pierfrancesco Leone, Pietro Carnevali, Clorinda Ciafardini, Giulio Petrocelli, Federica Mascaretti, Barbara Oreggia, Lorenzo Dioscoridi, Federica Cavalcoli, Massimo Primignani, Francesco Pugliese, Paola Bertuccio, Pietro Soru, Carmelo Magistro, Giovanni Ferrari, Michela C. Speciani, Giulia Bonato, Marta Bini, Paolo Cantu, Flavio Caprioli, Marcello Vangeli, Edoardo Forti, Stefano Mazza, Giulia Tosetti, Rossella Bonzi, Maurizio Vecchi, Carlo La Vecchia, Marta Rossi
Summary: In colorectal cancer patients, there is an overrepresentation of bacterial DNA in blood, which can potentially be used as a non-invasive diagnostic tool for early CRC detection. The gut microbiota and bacterial taxa are associated with CRC risk and can predict the presence of colon cancer with an accuracy of 0.70. These findings suggest a higher passage of bacteria from the gastrointestinal tract to the bloodstream in colon cancer patients, supporting the development of non-invasive diagnostic tests for colon cancer control.
Article
Environmental Sciences
Xinyu Yi, Chen Ning, Shuailong Feng, Haiqiang Gao, Jianlun Zhao, Juyang Liao, Yinghe Peng, Shuqing Zhao, Shuguang Liu
Summary: The study investigated the impact of urbanization intensity on soil bacterial communities in wetlands, and found significant changes in composition and diversity. pH and ammonia nitrogen were identified as the main environmental drivers. The results emphasize the importance of urbanization on wetland ecosystems and the role of environmental variables.
ENVIRONMENTAL RESEARCH LETTERS
(2022)
Article
Environmental Sciences
Kusum Dhakar, Shlomit Medina, Hamam Ziadna, Karam Igbaria, Guy Achdari, Ran Lati, Raphy Zarecki, Zeev Ronen, Guy Dovrat, Hanan Eizenberg, Shiri Freilich
Summary: Microbial communities in different crop fields respond differently to the application of the herbicide atrazine, as revealed by 16S rRNA gene amplicon sequencing. The nutrient-poor soil showed a different response compared to the nutrient-rich soils, both in terms of atrazine persistence and its effect on bacterial community structure and composition. Specific bacterial degraders of atrazine were more abundant in the contaminated nutrient-poor soil, while bacteria involved in nitrogen cycling were more abundant in the contaminated nutrient-rich soil. Understanding these responses can help in designing precision application strategies.
ENVIRONMENTAL RESEARCH
(2023)
Article
Microbiology
Christian O'Dea, Roger Huerlimann, Nicole Masters, Anna Kuballa, Cameron Veal, Paul Fisher, Helen Stratton, Mohammad Katouli
Summary: The study revealed rich and diverse gut microbiota in Australian Eastern Grey Kangaroos, with variations in microbial diversity profiles among kangaroos from different regions, suggesting environmental factors may impact their microbial composition.
Article
Immunology
Bridget S. Fisher, Katherine A. Fancher, Andrew T. Gustin, Cole Fisher, Matthew P. Wood, Michael Gale, Benjamin J. Burwitz, Jeremy Smedley, Nichole R. Klatt, Nina Derby, Donald L. Sodora
Summary: Liver disease is a major cause of illness and death in HIV-infected individuals. This study found that gut dysbiosis and microbial translocation can lead to changes in the liver microbiome, even during successful antiretroviral therapy. Specifically, an increase in Mycobacterium bacteria was observed in both SIV-infected and SIV-treated macaques. Additionally, the activation of inflammatory responses in liver cells was associated with immune cell recruitment in SIV-infected and treated macaques.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Environmental Sciences
Javiera Collao, Maria del Mar Morales-Amaral, Francisco Gabriel Acien-Fernandez, Silvia Bolado-Rodriguez, Nuria Fernandez-Gonzalez
Summary: The study showed that biomass productivity in photobioreactors increased as water depth decreased, but a decrease in bacterial community evenness may lead to a reduction in nutrient removal. Heterotrophs and phototrophs, mainly from the family Rhodobacteraceae, dominated bacterial diversity, and community changes were driven by various environmental factors and biological interactions.
Article
Ecology
Molly A. Moynihan, Nathalie F. Goodkin, Kyle M. Morgan, Phyllis Y. Y. Kho, Adriana Lopes dos Santos, Federico M. Lauro, David M. Baker, Patrick Martin
Summary: Despite low N-2 fixation rates, coral-associated diazotrophs supply a significant portion of the holobiont's nitrogen demand, particularly in the endolithic community. The activity of diazotrophs is mainly controlled by oxygen, with endolithic microbes playing a major role in coral nitrogen cycling.
Article
Ecology
Alfred Burian, Daisy Pinn, Ignacio Peralta-Maraver, Michael Sweet, Quentin Mauvisseau, Ozge Eyice, Mark Bulling, Till Roethig, Pavel Kratina
Summary: Experimental manipulation of protozoan predation pressure in activated sludge communities had strong and positive effects on bacterial diversity components, with responses leveling off at higher predation pressure levels. While predator intensity positively impacted taxa richness, predator diversity had mixed effects on bacterial diversity. Reduction in top-down control by predators negatively affected taxa associated with treatment efficiency, particularly nitrogen removal. The study highlights distinct mechanisms linking protozoan predation with bacterial diversity and community composition in activated sludge communities.
Article
Ecology
Monica Medina, David M. Baker, David A. Baltrus, Gordon M. Bennett, Ulisse Cardini, Adrienne M. S. Correa, Sandie M. Degnan, Gregor Christa, Eunsoo Kim, Jingchun Li, David R. Nash, Ezequiel Marzinelli, Michele Nishiguchi, Carlos Prada, Melissa S. Roth, Mahasweta Saha, Christopher I. Smith, Kevin R. Theis, Jesse Zaneveld
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
John L. Richards, Victoria Sheng, Haze Wing Yi Chung, Min Liu, Rainbow Hin Hung Tsang, Shelby E. McIlroy, David Baker
Summary: Fish and fishery products are highly traded commodities, but over-exploitation threatens their sustainability. Current monitoring techniques have limitations in assessing fish species. To address this, researchers developed an eDNA-based method to identify fish taxa from effluent water. Results showed that eDNA methods could overcome challenges of visual identification and provide an efficient and accurate market-wide species inventory.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Review
Microbiology
Raquel S. Peixoto, Christian R. Voolstra, Michael Sweet, Carlos M. Duarte, Susana Carvalhol, Helena Villela, Jeantine E. Lunshof, Lone Gram, Douglas C. Woodhams, Jens Walter, Anna Roik, Ute Hentschel, Rebecca Vega Thurber, Brendan Daisley, Blake Ushijima, Daniele Daffonchio, Rodrigo Costa, Tina Keller-Costa, Jeff S. Bowman, Alexandre S. Rosado, Gregor Reid, Christopher E. Mason, Jenifer B. Walker, Torsten Thomas, Gabriele Berg
Summary: Global biodiversity loss and mass extinction of species have become crucial environmental issues, leading to disruptions in various ecosystems and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse biodiversity deterioration and enhance wildlife and ecosystem resilience. However, implementation of these interventions is urgently needed. This article summarizes concepts, challenges, and ethical aspects of microbiome stewardship, which involves managing ecosystem resources responsibly to restore organisms and ecosystem functions. A framework guiding the application of environmental and wildlife probiotics is proposed, with consideration of risks versus the consequences of inaction. Careful and responsible microbiome management is critical to counteract biodiversity loss, but practical and regulatory obstacles must be addressed to maximize its effectiveness.
NATURE MICROBIOLOGY
(2022)
Article
Microbiology
Jie Li, Yiyang Zou, Jian Yang, Qiqi Li, David G. Bourne, Michael Sweet, Cong Liu, Anjie Guo, Si Zhang
Summary: Improving the availability of representative isolates from the coral microbiome is essential for investigating symbiotic mechanisms and applying beneficial microorganisms to improve coral health. In this study, a total of 395 bacterial strains were isolated from the coral Pocillopora damicornis, with most of them representing potential novel species or genera. Genomic information derived from the isolates identified putative metabolic functions and various genes associated with establishing association with the coral host. This work expands on the existing culture collection of coral-associated bacteria and provides important information on the metabolic potential of these isolates.
Review
Microbiology
Giulia Puntin, Michael Sweet, Sebastian Fraune, Monica Medina, Koty Sharp, Virginia M. Weis, Maren Ziegler
Summary: Stony corals form the foundation of coral reefs, which are significant ecosystems in both ecological and economic aspects. However, climate change and other human-induced stressors pose threats to the existence of these ecosystems, leading to coral bleaching, disease, and ultimately coral mortality. Despite extensive research, the underlying mechanisms and potential solutions to these destructive phenomena are still not fully understood.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2022)
Article
Marine & Freshwater Biology
Giulia Puntin, Jamie Craggs, Roisin Hayden, Kara E. E. Engelhardt, Shelby McIlroy, Michael Sweet, David M. M. Baker, Maren Ziegler
Summary: Reef-building corals rely on symbiosis with unicellular algae for their evolutionary success, but frequent heat waves cause coral mass-bleaching events, posing a serious threat to reef ecosystems. Understanding the functioning, breakdown, and prevention of coral-algal symbiosis remains incomplete due to difficulties in experimental handling and manipulating the association. The study identifies the stony coral species Galaxea fascicularis as a novel candidate coral model system, which allows for genotype studies and experimental investigation of the symbiosis.
Review
Marine & Freshwater Biology
Anthony M. M. Bonacolta, Bradley A. A. Weiler, Teresa Porta-Fito, Michael Sweet, Patrick Keeling, Javier del Campo
Summary: Many corals have a symbiotic relationship with photosynthetic dinoflagellates, but the role of microeukaryotes like protists and fungi in the coral holobiont and reef ecosystems is not well understood. Recent advances in metabarcoding have highlighted the importance of microeukaryotes in corals, and it is necessary to present the current knowledge before further studies are conducted.
Article
Biodiversity Conservation
Reanne Bower, Mark Bulling, Briony Norton
Summary: This article aims to raise awareness of the overlooked insect group of Bombus subgenus Psithyrus and advocate for vital research in targeted conservation efforts. Despite forming approximately 11% of Bombus species, Psithyrus has received little academic attention, with less than 2% of the total works on Bombus focusing on it. The study argues that Psithyrus species play important roles in ecosystems and have the potential to serve as bioindicators of Bombus diversity. Research on Psithyrus distributions and phenology is crucial for conservation efforts and provides opportunities to enhance our understanding of ecosystem dynamics and their links to ecosystem services under climate change.
JOURNAL OF INSECT CONSERVATION
(2023)
Article
Marine & Freshwater Biology
Henrique Bravo, J. Antonio Baeza, Sancia E. T. van der Meij
Summary: This study conducted the first genomic survey and complete mitochondrial assemblage and characterization of the elkhorn coral crab Domecia acanthophora. The results revealed the size of its nuclear genome, the composition of repetitive elements, and the structure of its mitochondrial genome.
JOURNAL OF CRUSTACEAN BIOLOGY
(2023)
Article
Marine & Freshwater Biology
Henrique Bravo, Ian R. Tibbetts
Summary: An experiment was conducted to determine the potential role of Clibanarius corallinus as a mesograzer in coral reef ecosystems. The results showed that hermit crabs can remove epilithic algae, resulting in a decrease in chlorophyll content on coral fragments exposed to them. The detritus generated by the crabs had higher chlorophyll content and lower organic biomass compared to the control environment.
JOURNAL OF CRUSTACEAN BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Tao Xu, Henrique Bravo, Sancia E. T. van der Meij
Summary: Through the study of the mitochondrial genomes of gall crabs, the phylogenetic relationships and evolutionary history of symbiotic relationships in this group were revealed. The study also found differences in gene order between symbiotic and free-living species, and suggested that the adaptive evolution of mitochondrial protein-coding genes may be related to the energetic demands of a symbiotic lifestyle.
Article
Marine & Freshwater Biology
Sancia E. T. Van der Meij, Henrique Bravo, Yun J. H. Scholten, Charlotte R. Dromard
Summary: Coral-dwelling crabs form a diverse community on coral reefs, and different families independently colonise different species of coral. This study provides an overview of all known hosts of Domecia species and creates the first phylogeny of the genus using molecular data. Domecia acanthophora shows less host specificity compared to its Indo-Pacific counterparts.
CAHIERS DE BIOLOGIE MARINE
(2022)