Article
Marine & Freshwater Biology
Patricia Gomez-Villegas, Jose Luis Guerrero, Miguel Perez-Rodriguez, Juan Pedro Bolivar, Antonio Morillo, Javier Vigara, Rosa Leon
Summary: This study investigated the microbial community in phosphogypsum (PG) deposits in Huelva, Spain and identified a diverse range of microbial species that can thrive in the extreme acidic and polluted environment. The study also discovered the presence of algae, fungi, and ciliates in the PG stacks. The findings suggest that the microbial community in these PG deposits may play a significant role in the dynamics of contaminating compounds and have potential for biotechnological applications.
AQUATIC TOXICOLOGY
(2022)
Article
Microbiology
Jasmin L. Millar, Elizabeth A. Bagshaw, Arwyn Edwards, Ewa A. Poniecka, Anne D. Jungblut
Summary: Cryoconite holes, containing water and microbe-mineral aggregates, are hotspots of microbial diversity on glacial surfaces. They form in various conditions and locations, impacting their structure and community composition. The bacterial and microalgal communities in Arctic and Antarctic cryoconite holes show clear divisions, with regionally distinct microbial communities adapted to differing conditions within the cryosphere.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biodiversity Conservation
Anais Chanson, Corrie S. Moreau, Christophe Duplais
Summary: This study examines the impact of host ecology and evolutionary history on the microbial communities of Amazonian ants. The research shows that habitat does not play a role in structuring ant microbial communities, but ant diet and nesting mode do influence bacterial communities. Additionally, nesting mode is the determining factor for microbial eukaryote communities, while microbial diversity is not correlated with host phylogeny.
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
Ecology
Ulrike Obertegger, Massimo Pindo, Giovanna Flaim
Summary: The study compared microscopy and high-throughput sequencing in detecting and quantifying algae, exploring the differences between these methods and their impact on ecological inferences of phytoplankton communities. By analyzing phytoplankton communities of Lake Tovel in Italy, the researchers found that HTS data provided more detailed information compared to microscopy, and highlighted the effects of methodological, habitat, and year differences on the study results. Additionally, redundancy analyses indicated the importance of hydrology, nutrients, and temperature for phytoplankton communities, with HTS showing higher variance explained and microscopy distinguishing habitat types differently. Ultimately, despite metric effects, HTS-based data supported the potential of becoming a key tool for biodiversity research.
FRESHWATER BIOLOGY
(2021)
Article
Environmental Sciences
Yan Wei, Yumeng Li, Yayu Wang, Xinyue Luo, Feirong Du, Weifang Liu, Li Xie, Jianwei Chen, Ziwei Ren, Shiqi Hou, Sunhaoyu Wang, Shaojie Fu, Yan Dang, Pengsong Li, Xin Liu
Summary: This study explored the microbial diversity in industrial effluents and verified the feasibility of tracking these effluents in sewer networks based on sequencing data. The results showed that microbial compositions varied greatly among samples from different locations in the sewer system. Furthermore, the study identified microbial markers that differentiate effluents from different factories, which can be used to track the sources of the effluents.
ENVIRONMENTAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Marie-Pierre Chapuis, Laure Benoit, Maxime Galan
Summary: Obtaining high-quality nucleic acids is crucial for studying bacterial communities associated with animal hosts. This study compared five DNA extraction protocols for animal samples using different methods, including mechanical or enzymatic lysis. The results showed that none of the methods fully eliminated bias, but one method with enzymatic lysis had lower bias. Standardization of DNA extraction is important for comparing microbiome results across different samples.
MOLECULAR ECOLOGY RESOURCES
(2023)
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
Microbiology
Hiu-Yin Lao, Timothy Ting-Leung Ng, Ryan Yik-Lam Wong, Celia Sze-Ting Wong, Lam-Kwong Lee, Denise Sze-Hang Wong, Chloe Toi-Mei Chan, Stephanie Hoi-Ching Jim, Jake Siu-Lun Leung, Hazel Wing-Hei Lo, Ivan Tak-Fai Wong, Miranda Chong-Yee Yau, Jimmy Yiu-Wing Lam, Alan Ka-Lun Wu, Gilman Kit-Hang Siu
Summary: In this study, two 16S rRNA gene sequencing tests based on the Illumina and Nanopore sequencing technologies were compared to identify clinical isolates that cannot be identified by MALDI-TOF MS. The results showed that the Nanopore workflow had a higher taxonomic resolution at the species level.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Food Science & Technology
Creciana M. Endres, Icaro Maia S. Castro, Laura D. Trevisol, Juliana M. Severo, Michele B. Mann, Ana Paula M. Varela, Ana Paula G. Frazzon, Fabiana Q. Mayer, Jeverson Frazzon
Summary: Microbial communities in sheep's milk and cheese vary between different geographic regions, with significant differences in diversity observed among different types of cheeses. Processing and maturation conditions play a key role in shaping cheese microbiota. Other bacterial groups, including potentially pathogenic microorganisms to humans, were also identified in some cheeses analyzed.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Veterinary Sciences
Haigang Wu, Xian Wu, Li Huang, Chongmei Ruan, Jinni Liu, Xiaoqing Chen, Jicheng Liu, Houqing Luo
Summary: This study found that andrographolide administration increased the proportions and abundance of beneficial bacteria, while amoxicillin treatment increased the proportion of pathogenic bacteria. The results suggest potential alternatives to antibiotics for reducing bacterial resistance and restoring intestinal flora balance.
FRONTIERS IN VETERINARY SCIENCE
(2021)
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
Biochemistry & Molecular Biology
Babett Guenther, Sophie Marre, Clemence Defois, Thomas Merzi, Philippe Blanc, Pierre Peyret, Sophie Arnaud-Haond
Summary: Biodiversity inventory of marine systems is constrained by unbalanced access to different oceanic dimensions. The utilization of eDNA for metabarcoding shows promise as a future biodiversity research tool, but challenges remain in interpreting results due to gaps in reference databases and PCR bias. By using the capture by hybridization (CBH) approach and targeting 18S rDNA, this study successfully demonstrated an improved method for detecting metazoans in marine ecosystems, providing a valuable tool for biodiversity assessments in data-poor environments such as the deep sea.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biotechnology & Applied Microbiology
Eiseul Kim, Eun-Ji Cho, Seung-Min Yang, Mi-Ju Kim, Hae-Yeong Kim
Summary: A study compared culture-dependent and culture-independent methods for identifying microbial community changes during kimchi fermentation. Both methods identified Lactobacillus-related genera, Leuconostoc, and Weissella as predominant microorganisms, with the culture-independent method additionally identifying non-lactic acid bacteria and yeasts. The culture-dependent method could identify species level and predominant species in viable cell communities, while culture-independent method provided a more comprehensive view of the microbial ecology in fermented kimchi.
Article
Marine & Freshwater Biology
Lidia Yebra, Candela Garcia-Gomez, Nerea Valcarcel-Perez, Alma Hernandez de Rojas, Leocadio Blanco-Bercial, M. Carmen Castro, Francisco Gomez-Jakobsen, Jesus M. Mercado
Summary: This study characterized the variability in composition and structure of mesozooplankton communities in the Bay of Malaga using an integrative taxonomic approach. The combination of microscopic identification and metabarcoding allowed for higher resolution in species identification and broader taxonomic coverage. Differences in zooplankton communities between coastal-night and shelf-day were detected using both microscopy and metabarcoding. The integrative approach increased the knowledge of copepod species in the Southwest Mediterranean Sea by 9%.
ESTUARINE COASTAL AND SHELF SCIENCE
(2022)
Article
Environmental Sciences
John K. Pearman, Susanna A. Wood, Marcus J. Vandergoes, Javier Atalah, Sean Waters, Janet Adamson, Georgia Thomson-Laing, Lucy Thompson, Jamie D. Howarth, David P. Hamilton, Xavier Pochon, Laura Biessy, Katie A. Brasell, Jenny Dahl, Riki Ellison, Sean J. Fitzsimons, Henry Gard, Tania Gerrard, Rose Gregersen, McKayla Holloway, Xun Li, David J. Kelly, Reece Martin, Kiely McFarlane, Nicholas P. McKay, Adelaine Moody, Chris M. Moy, Sebastian Naeher, Rewi Newnham, Russleigh Parai, Mailys Picard, Jonathan Puddick, Andrew B. H. Rees, Lizette Reyes, Marc Schallenberg, Claire Shepherd, Julia Short, Kevin S. Simon, Konstanze Steiner, Charlotte Sunde, Marianna Terezow, John Tibby
Summary: Efficient monitoring methods for lakes are necessary for proactive protection and management. Using bacterial communities in lake surface sediments provides a rapid and cost-effective way to assess trophic states.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Mailys Picard, Xavier Pochon, Javier Atalah, John K. Pearman, Andrew Rees, Jamie D. Howarth, Christopher M. Moy, Marcus J. Vandergoes, Ian Hawes, Samiullah Khan, Susanna A. Wood
Summary: The frequency and intensity of cyanobacterial blooms is increasing worldwide, with most of the factors implicated being anthropogenic. The study conducted in New Zealand revealed the impacts of human settlement on lake ecosystems by reconstructing cyanobacterial communities over the last 1000 years. It was discovered that cyanobacteria were already present in the lakes before human arrival, but their abundance and richness significantly increased after European settlement, particularly in lakes where bloom-forming taxa became dominant.
SCIENTIFIC REPORTS
(2022)
Article
Limnology
John K. Pearman, Janet Adamson, Georgia Thomson-Laing, Lucy Thompson, Sean Waters, Marcus J. Vandergoes, Jamie D. Howarth, Susanna A. Wood
Summary: Biological communities in lake surface sediments are crucial for biogeochemical cycling and ecosystem services. This study investigated abundance-occupancy patterns and assembly processes of bacteria and eukaryotes across a large spatial scale and multiple environmental gradients. The results provide new insights into the ecology of these organisms and the effects of environmental stressors on lake sediment communities.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Paleontology
Bruce W. Hayward, Ashwaq T. Sabaa, Jamie D. Howarth, Alan R. Orpin, Lorna J. Strachan, Stephanie E. Tickle
Summary: The 2016 Kaikoura Earthquake triggered turbidity currents down submarine canyons along the east of New Zealand. The foraminiferal samples from these currents provide insights into the complexities of submarine gravity flows. The variability of foraminiferal fragmentation index values suggests that test breakage in turbidite samples is primarily inherited from dissolution on the seafloor. The faunas in both turbidite and pre-turbidite sediments show strong signatures of downslope displacement, and pre-turbidite faunas can be distinguished from the 2016 turbidites' faunas by their different planktic percentages and shallow to deep benthic test ratios. Intra-turbidite faunal variability can be attributed to factors such as erosion, entrainment, and test-size sorting during transport and deposition.
MARINE MICROPALEONTOLOGY
(2022)
Article
Geosciences, Multidisciplinary
Marine Le Minor, Philippe Davy, Jamie Howarth, Dimitri Lague
Summary: In natural rivers, the diversity of transport modes is controlled by sediment heterogeneity and flow variability. However, there is currently a lack of a law that can explain sediment transport from bed load to suspended load for a wide range of sediment mixtures and flow conditions. In this study, we present a Multi Grain-Size Total Load model that captures the diversity of transport modes and predicts transport capacities for different grain sizes based on widely accepted concepts of sediment transport.
JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE
(2022)
Article
Geochemistry & Geophysics
Sean Waters, Javier Atalah, Lucy Thompson, Georgia Thomson-Laing, John K. Pearman, Jonathan Puddick, Jamie D. Howarth, Lizette Reyes, Marcus J. Vandergoes, Susanna A. Wood
Summary: Lake ecosystems worldwide are experiencing eutrophication and degradation due to human activities. Limited data hinders the understanding of lake health at national scales, making long-term monitoring impractical. Analyzing sediment geochemistry provides an efficient method for assessing contemporary water quality and predicting trophic levels in unmonitored lakes.
APPLIED GEOCHEMISTRY
(2023)
Article
Geography, Physical
Stephen B. Piva, Simon J. Barker, Rewi M. Newnham, Andrew B. H. Rees, Colin J. N. Wilson, Lionel Carter, Nels A. Iverson, Benjamin Läuchli, Paul C. Augustinus
Summary: This study analyzed sediment cores from Onepoto maar palaeolake in Auckland to investigate the impacts of the Oruanui supereruption on vegetation and landscape. The results showed that the eruption caused partial defoliation of canopy trees, allowing more light penetration and promoting sub-canopy vegetation growth. This study also demonstrated the value of millimeter-scale stratigraphic pollen analysis for assessing eruptive impacts on sub-decadal timescales.
JOURNAL OF QUATERNARY SCIENCE
(2023)
Article
Geography, Physical
Charlotte O. Pizer, Jamie D. Howarth, Kate J. Clark, Colin J. N. Wilson, Stephanie E. Tickle, Jenni L. Hopkins, Jenny A. Dahl
Summary: Volcanic ash (tephra) horizons are important for correlating natural archives, but age uncertainties can hinder their effectiveness. We use the Waimihia tephra as a case study to improve age constraints for Holocene tephra isochrons by employing detailed assessments, precise AMS dating, and Bayesian age models. Our findings have implications for refining paleoearthquake correlations and chronologies relying on the Waimihia isochron.
QUATERNARY SCIENCE REVIEWS
(2023)
Article
Environmental Sciences
Rose Gregersen, Jamie D. Howarth, Javier Atalah, John K. Pearman, Sean Waters, Xun Li, Marcus J. Vandergoes, Susanna A. Wood
Summary: Lakes are important for ecosystem services and biodiversity, but cultural eutrophication remains a major threat to their health. The lack of long-term monitoring records limits our ability to manage lake eutrophication. This study developed a bio-indicator approach using diatom communities to infer trophic levels in lakes, and the results were consistent with monitoring data and land-use histories. However, recent shifts in diatom communities were not captured by traditional trophic level indices, highlighting the importance of new approaches in preventing the decline of lake ecosystems worldwide.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biology
Georgia Thomson-Laing, Lena Schallenberg, David Kelly, Jamie D. Howarth, Susanna A. Wood
Summary: Freshwater fish are facing a perilous situation, as more than 30% of species are critically endangered. However, determining the impact of disturbances on native fish communities is challenging due to ecological and methodological complexities. This review examines current methods used to assess the responses of fish communities, particularly in lakes, and identifies knowledge gaps and challenges. The authors advocate for an integrative approach that combines emerging technologies and underutilized knowledge streams, alongside conventional methods, to enable more informed and effective management actions.
BIOLOGICAL REVIEWS
(2023)
Article
Marine & Freshwater Biology
Jonathan Puddick, Sebastian Naeher, John K. Pearman, Carrie D. Page, Donato Romanazzi, Lena A. Schallenberg, Jamie D. Howarth, Marcus J. Vandergoes, Susanna A. Wood
Summary: Cyanobacterial blooms are increasing globally, impacting lake ecosystems and posing a risk to human and animal health. Cyanobacterial pigments preserved in lake sediments can help understand the changes that have led to these blooms. By analyzing pigments in cyanobacteria cultures and applying the findings to lake sediments, we found that carotenoids can be used to evaluate cyanobacterial abundance and differentiate different cyanobacteria types. Ratios of specific carotenoids can be used as a proxy to evaluate historical shifts in cyanobacterial communities.
Article
Environmental Sciences
Rose Gregersen, John K. Pearman, Javier Atalah, Sean Waters, Marcus J. Vandergoes, Jamie D. Howarth, Georgia Thomson-Laing, Lucy Thompson, Susanna A. Wood
Summary: Anthropogenic eutrophication, a pressing issue for lakes globally, is difficult to manage due to limited monitoring records. This study presents a taxonomy-free diatom-based biomonitoring method using environmental DNA metabarcoding data, offering an accurate and automated alternative for eutrophication monitoring.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)