Article
Microbiology
James O'Brien, Erin L. McParland, Anna R. Bramucci, Martin Ostrowski, Nachshon Siboni, Timothy Ingleton, Mark V. Brown, Naomi M. Levine, Bonnie Laverock, Katherina Petrou, Justin Seymour
Summary: This study examines the relationship between microbial community dynamics and DMS concentrations in an oceanographic time series conducted on the east Australian coast. The results show that seasonal shifts in microbial community composition affect the net DMSP concentrations, with certain phytoplankton species producing more DMSP than others. Additionally, planktonic bacteria play a significant role in producing DMSP and DMSO in ocean surface waters.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Cecilia Costas-Selas, Sandra Martinez-Garcia, Ramiro Logares, Marta Hernandez-Ruiz, Eva Teira
Summary: This study provides the first detailed description of the seasonal patterns in bacterial community composition (BCC) in shelf waters off the Ria de Vigo (Spain). The study also reveals strong correlations between BCC and small-sized eukaryotic community composition (ECC), suggesting the importance of biotic interactions in structuring the microbial plankton in this productive area.
Article
Microbiology
Ningning Xu, Wenlei Wang, Kai Xu, Yan Xu, Dehua Ji, Changsheng Chen, Chaotian Xie
Summary: This study investigated the effects of seasons and different seaweed species on microbial communities. The results showed that environmental factors in seaweed cultivation zones significantly influenced the variability of fungal and bacterial communities. Certain microbial groups responded positively to seaweed cultivation, and their enrichment was influenced by the composition of dissolved organic matter (DOM).
FRONTIERS IN MICROBIOLOGY
(2022)
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
Parasitology
Sandor Hornok, Andrei D. Mihalca, Jeno Kontschan, Nora Takacs, Denis Fedorov, Olivier Plantard, Attila D. Sandor
Summary: This study provides high-resolution digital pictures and molecular data of male and female I. rugicollis for the first time, and morphological comparison with I. cornutus could not resolve uncertainties in the latter species' validity. Further molecular comparisons with new specimens of I. cornutus are needed to confirm its status. This study represents the first comprehensive molecular phylogenetic analysis of western Palearctic Pholeoixodes species, including I. rugicollis, and confirms the phylogenetic position of the subgenus Eschatocephalus within Pholeoixodes.
PARASITES & VECTORS
(2023)
Article
Microbiology
Sania Arif, Corinna Willenberg, Annika Dreyer, Heiko Nacke, Michael Hoppert
Summary: The microbial communities in the hydrothermal steam environment of Sasso Pisano exhibit high metabolic diversity, with a higher capability to utilize methane and aromatic compounds, as well as a more diverse sulfur and nitrogen metabolism compared to mesophilic soil microbes. Additionally, heavy metal resistance genes are more abundant in the hot spring microbiome, while the eukaryotic diversity at a fumarole suggests a simplified food web in an extremely nutrient-deprived acidic environment.
Article
Food Science & Technology
Niki Mougiou, Antiopi Tsoureki, Spyros Didos, Ioanna Bouzouka, Sofia Michailidou, Anagnostis Argiriou
Summary: The analysis of table olives microbiome using next-generation sequencing has provided valuable information about the microbial community composition of this popular fermented food. This study used 16S and 18S rRNA sequencing to evaluate the microbial communities of table olives from five Greek popular cultivars, fermented by Greek or Spanish style. The results showed that different curing and fermentation methods had an impact on the microbial composition and biochemical properties of the olives.
Article
Biotechnology & Applied Microbiology
Julia A. Gustavsen, Curtis A. Suttle
Summary: This study revealed that the composition of marine viral assemblages undergoes significant changes over time and is laggedly correlated with the resemblance of potential hosts, indicating the influence of viruses on host communities. The dominant clusters of phylogenetically related viruses shift over time, reflecting ecological dynamics within these clusters. The temporal shuffling of viral genotypes primarily occurs within a few subsets of related individuals, suggesting a common structure in natural viral assemblages.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Peeter Laas, Kelly Ugarelli, Rafael Travieso, Sandro Stumpf, Evelyn E. Gaiser, John S. Kominoski, Ulrich Stingl
Summary: Planktonic microbial communities in wetland ecosystems play a vital role, yet they are relatively underexplored compared to other aquatic ecosystems. This study conducted a high-resolution analysis of bacterial and eukaryotic microbial communities in the Florida Everglades, revealing significant variations along the salinity gradient.
Article
Soil Science
Ilonka C. Engelhardt, Pascal A. Niklaus, Florian Bizouard, David Bru, Marie -Christine Breuil, Nadine Rouard, Arnaud Mounier, Laurent Philippot, Romain L. Barnard
Summary: This study found that precipitation history has an impact on the microbial community's response to rewetting, which is related to the nitrogen status. Regardless of precipitation or nitrogen input history, active bacteria showed a small shift in community composition within 1 hour of rewetting, but did not change further for the remaining 28 hours analyzed. Active fungi did not respond to rewetting within 29 hours. These findings are important for understanding the short-term response of soil microbial communities and their effects on food web stability and soil biogeochemical cycling.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Marine & Freshwater Biology
Francesco Ricci, Alexander Fordyce, William Leggat, Linda L. Blackall, Tracy Ainsworth, Heroen Verbruggen
Summary: The study characterized the endolithic microbial community of the common coral Isopora palifera in the Great Barrier Reef, revealing the abundance of oxygenic photosynthetic endolithic microbes, including chlorophyll a. The bacterial community was mainly composed of Proteobacteria, Bacteroidetes, Actinobacteria, and Spirochaetes, while the micro-eukaryotic community was dominated by endolithic green algae and the protist Labyrynthula at high relative abundance.
Article
Microbiology
Elizabeth D. Swanner, Marina Wuestner, Tania Leung, Jurgen Pust, Micah Fatka, Nick Lambrecht, Hannah E. Chmiel, Harald Strauss
Summary: This study investigates the relationship between dissolved iron and the subsurface chlorophyll maxima layers (SCML) in a freshwater lake. The results show that, despite higher chlorophyll abundance in the spring, the SCML is located below the primary productivity maximum within the epilimnion. In the fall, the SCML is associated with elevated dissolved iron concentrations and a local maximum in carbon isotope δC-13(DIC). Cyanobacteria and Chlorophyta are more abundant within the SCML in the fall.
Article
Geosciences, Multidisciplinary
Tiago de Oliveira Santos, Felipe Jose Cury Fracetto, Valdomiro Severino de Souza Junior, Jose Coelho de Araujo Filho, Mario Andrade Lira Junior, Jose Petronio Mendes Junior, Marcos Siqueira Neto, Yure Romero Oliveira da Silva, Felipe Martins do Rego Barros, Giselle Gomes Monteiro Fracetto
Summary: Overexploitation of natural forest resources in the tropical semiarid region of Brazil leads to soil degradation, reduction in microbial and plant biomass, and loss of C and N from soils. This study found that degraded soils had significantly lower C and N stocks, abundance and activity of total bacteria and fungi, and decreased abundance of diazotrophic and phosphorus-mineralizing bacteria compared to preserved or partially degraded soils. However, the abundance of total bacteria and fungi genes and glomalin content remained unchanged. The alkaline phosphatase activity indicated that mineralizing microorganisms can still make phosphorus constantly available in soils without vegetation cover.
Article
Environmental Sciences
Blaire M. Padayhag, Michael Angelou L. Nada, Jake Ivan P. Baquiran, Marilou P. Sison-Mangus, Maria Lourdes San Diego-McGlone, Patrick C. Cabaitan, Cecilia Conaco
Summary: This study found that the microbial biofilm communities near mariculture areas can affect the settlement of coral larvae. The biofilm farthest from the mariculture area had a higher effectiveness in inducing the settlement of Acropora tenuis larvae. These biofilms were characterized by a greater proportion of crustose coralline algae and gammaproteobacterial taxa, while biofilms closer to the mariculture zone had a higher proportion of cyanobacteria and no crustose coralline algae. These findings suggest that nutrient enrichment from mariculture activities can alter the composition of biofilm-associated microbiome and indirectly affect coral larval settlement.
MARINE POLLUTION BULLETIN
(2023)
Article
Microbiology
Dandan Yu, Jinru Yang, Min Jin, Bin Zhou, Linli Shi, Lei Zhao, Jieying Zhang, Zhenyu Lin, Jinghua Ren, Li Liu, Tao Zhang, Hongli Liu
Summary: The gut microbiome plays a critical role in predicting gastric cancer and liver metastasis, with Streptococcus potentially serving as a biomarker.
Article
Ecology
Edward B. Rastetter, George W. Kling, Gaius R. Shaver, Byron C. Crump, Laura Gough, Kevin L. Griffin
Summary: This study presents a framework for assessing the biogeochemical recovery of terrestrial ecosystems from disturbances, outlining three recovery phases. The level of openness of the nitrogen cycle, nitrogen distribution in vegetation and soils, and the proportion of nitrogen losses in a refractory form all play key roles in influencing recovery trajectories. High openness exacerbates initial nitrogen losses but accelerates later recovery phases, while a high fraction of ecosystem nitrogen in vegetation can have a similar effect. Additionally, a high proportion of nitrogen loss in a refractory form mitigates initial nitrogen losses and speeds up recovery in later phases.
Article
Multidisciplinary Sciences
Scott Zolkos, Alexander V. Zhulidov, Tatiana Yu. Gurtovaya, Vyacheslav V. Gordeev, Sergey Berdnikov, Nadezhda Pavlova, Evgenia A. Kalko, Yana A. Kuklina, Danil A. Zhulidov, Lyudmila S. Kosmenko, Alexander I. Shiklomanov, Anya Suslova, Benjamin M. Geyman, Colin P. Thackray, Elsie M. Sunderland, Suzanne E. Tank, James W. McClelland, Robert G. M. Spencer, David P. Krabbenhoft, Richard Robarts, Robert M. Holmes
Summary: High levels of methylmercury accumulation in marine biota in the Arctic are a concern. Recent research on Russian rivers shows a decline in particulate mercury concentrations and suspended solids, resulting in a significant reduction in mercury export to the Arctic Ocean.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Environmental Sciences
Hengchen Wei, Xin Xu, Allan E. Jones, Amber K. Hardison, Kevan B. Moffett, James W. McClelland
Summary: This study sheds light on the role of tidal freshwater zones (TFZs) in modifying the timing and forms of nitrogen (N) inputs to estuaries. The research found that median concentrations of dissolved inorganic N (DIN) were lower in TFZs compared to upstream non-tidal river reaches, and exhibited spatial gradients. The forms of N also changed within TFZs, with DIN transforming into organic N. Comparisons of discharge and N flux in the Aransas River TFZ showed that tidal patterns influenced the timing of N export, with export exceeding input in winter and being relatively balanced in summer.
ESTUARIES AND COASTS
(2022)
Article
Cell Biology
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides
Summary: This study used a large-scale comparative genomics approach to discover that small genes are more prevalent in phage genomes than in host prokaryotic genomes. These small genes may have important functions, such as encoding anti-CRISPR proteins and antimicrobial proteins.
Article
Environmental Sciences
Dawn R. URycki, Maoya Bassiouni, Stephen P. Good, Byron C. Crump, Bonan Li
Summary: This study assessed the extent to which microbial communities encode information about catchment hydrology across scales and found that many microbial taxa shared information with hydrologic metrics. The results demonstrate that microbial communities are rich sources of information that may contribute fresh insight to unresolved hydrologic questions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biotechnology & Applied Microbiology
Clara L. Mackenzie, Christopher M. Pearce, Sarah Leduc, Daniel Roth, Colleen T. E. Kellogg, Rute B. G. Clemente-Carvalho, Timothy J. Green
Summary: Shellfish industries worldwide are threatened by summer mortality events, often associated with Vibrio disease outbreaks. This study examines the impact of seawater pH buffering on the larval microbiome and subsequent adult susceptibility to mortality events. Findings show that even minimal buffering results in a changed microbiome and increased mortality under stressors, emphasizing the importance of hatchery practices in shaping resilience.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Marine & Freshwater Biology
Rose-Lynne Savage, Jacqueline L. Maud, Colleen T. E. Kellogg, Brian P. Hunt, Vera Tai
Summary: The eukaryotic microbiomes of dominant crustacean zooplankton from the Strait of Georgia were characterized using metabarcoding. Alveolates, predominantly ciliates and dinoflagellates, were found to be the dominant protists in all examined zooplankton. Symbiont lineages showed host preference, with Pseudocolliniidae ciliate parasites being associated with ostracods. Free-living protists, including diatoms and hydrozoans, were inferred to be part of the zooplankton diet, suggesting an underestimated pathway of carbon cycling.
JOURNAL OF PLANKTON RESEARCH
(2023)
Review
Ecology
Robert H. Hilderbrand, Ted Bambakidis, Byron C. Crump
Summary: The goods and services provided by riverine systems are vital for humanity, but these systems are degrading worldwide despite restoration efforts. Designing restorations to promote microbial communities could enhance restoration effectiveness. Focusing on microbial diversity and function can improve resilience and assess restoration suitability. Advancements in next-generation sequencing allow the use of microbial 'omics techniques to assess river ecological conditions and advance assessment capabilities.
Article
Microbiology
Jan F. Finke, Colleen T. E. Kellogg, Curtis A. Suttle
Summary: Deep6 is a deep learning model that accurately classifies short metatranscriptomic sequences into prokaryotes, eukaryotes, or viral realms, without the need for reference or alignment. The average accuracies range from 0.87 to 0.97, depending on the length of the sequences.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Engineering, Environmental
Cheng Shi, Gouri Mahadwar, Emmanuel Davila-Santiago, Ted Bambakidis, Byron C. Crump, Gerrad D. Jones
Summary: We investigated the factors that influence the variability in non-target chemical composition in riverine systems in Oregon. We found that the influence of microbial communities and environmental variables on chemical composition was greater than that of landscape gradients. Contrary to our hypothesis, there was little evidence to suggest that chemical variability was related to landscape gradients, but rather it was controlled by microbial and seasonal hydrologic processes. The results suggest the importance of ecosystem processes in shaping aquatic chemistry.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Megan I. Behnke, Suzanne E. Tank, James W. McClelland, Robert M. Holmes, Negar Haghipour, Timothy I. Eglinton, Peter A. Raymond, Anya Suslova, Alexander Zhulidov, Tatiana Gurtovaya, Nikita Zimov, Sergey Zimov, Edda A. Mutter, Edwin Amos, Robert G. M. Spencer, Andrea Rinaldo
Summary: Arctic rivers are important channels for transmitting signals of change from the changing landscape to the ocean. This study reveals a previously overlooked contribution from aquatic biomass in the particulate organic matter (POM) flux. It also suggests that climate change-induced warming and increasing CO2 concentrations could enhance soil destabilization and aquatic biomass production, leading to increased POM fluxes to the ocean.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Environmental Sciences
M. Kelsey Lane, Jennifer S. Fehrenbacher, Jennifer L. Fisher, Melanie R. Fewings, Byron C. Crump, Craig M. Risien, Grace M. L. Meyer, Faith Schell
Summary: Under future climate scenarios, it is predicted that marine heatwaves (MHW) will become more frequent and intense. However, little is known about the impact of these events on planktonic foraminifera, which are commonly used as paleoproxies. This study found that the composition and abundance of planktonic foraminifera in the Northern California Current varied during MHWs, suggesting that fossil foraminiferal assemblages may provide insights into past MHWs.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Marine & Freshwater Biology
Hengchen Wei, Xin Xu, Ally Savoie, Elizabeth Schattle, Amber K. Hardison, Deana L. Erdner, James W. Mcclelland
Summary: This study assessed the contribution of diverse phytoplankton groups to chlorophyll a biomass in tidal freshwater zones (TFZs) and investigated their relation with temperature, DIN, SRP, and DIN/SRP ratios. The results showed higher chl a levels in TFZs compared to the upstream river and downstream estuary, with cyanobacteria prominently contributing to chl a biomass, especially in the lower TFZ sections. This highlights the role of prolonged residence times and nutrient enrichment in TFZs, which result in elevated chl a concentrations and shape phytoplankton community composition, with implications for downstream estuaries.
Article
Geosciences, Multidisciplinary
Suzanne E. Tank, James W. McClelland, Robert G. M. Spencer, Alexander I. Shiklomanov, Anya Suslova, Florentina Moatar, Rainer M. W. Amon, Lee W. Cooper, Greg Elias, Vyacheslav V. Gordeev, Christopher Guay, Tatiana Yu. Gurtovaya, Lyudmila S. Kosmenko, Edda A. Mutter, Bruce J. Peterson, Bernhard Peucker-Ehrenbrink, Peter A. Raymond, Paul F. Schuster, Lindsay Scott, Robin Staples, Robert G. Striegl, Mikhail Tretiakov, Alexander V. Zhulidov, Nikita Zimov, Sergey Zimov, Robert M. Holmes
Summary: Rivers are sensitive indicators of watershed changes and regulate ecosystem function across the land-ocean continuum. A study on major Arctic rivers found that alkalinity and associated ion fluxes to the ocean increased significantly, while nitrate and other inorganic nutrient fluxes declined. Dissolved organic carbon fluxes showed no overall trend. This indicates disturbance of multiple land processes, with implications for coastal ocean biogeochemical cycling.
Article
Ecology
Karl J. Romanowicz, Byron C. Crump, George W. Kling
Summary: This study used quantitative metabarcoding and metagenomic sequencing to investigate the changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra in northern Alaska. The findings reveal that iron redox metabolism dominates microbial carbon degradation during permafrost thaw, leading to increased microbial respiration and suppression of methanogenesis.
ISME COMMUNICATIONS
(2023)