Article
Ecology
Emilie Lyautey, Elodie Billard, Nathalie Tissot, Stephan Jacquet, Isabelle Domaizon
Summary: This study investigated the spatial variability and temporal dynamics of methanogenic Archaea and methanotrophic bacteria in Lake Bourget, France. Changes in both structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics.
Article
Microbiology
Weigang Hu, Qingqing Hou, Manuel Delgado-Baquerizo, James C. Stegen, Qiajun Du, Longwei Dong, Mingfei Ji, Yuan Sun, Shuran Yao, Haiyang Gong, Junlan Xiong, Rui Xia, Jiayuan Liu, Muhammad Aqeel, Muhammad Adnan Akram, Jinzhi Ran, Jianming Deng
Summary: A study in northern China's drylands found that there are distinct distributions of archaea and ammonia-oxidizing archaea in the soil. Archaea are mainly found in deserts, while ammonia-oxidizing archaea are more abundant in grasslands. The distribution of archaea is primarily driven by environmental factors, while ammonia-oxidizing archaea are influenced by spatial factors.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Geosciences, Multidisciplinary
Jasmine S. Berg, Mathilde Lepine, Emile Laymand, Xingguo Han, Hendrik Vogel, Marina A. Morlock, Niroshan Gajendra, Adrian Gilli, Stefano M. Bernasconi, Carsten J. Schubert, Guangyi Su, Mark A. Lever
Summary: This study comprehensively investigates the deep lacustrine biosphere in Lake Cadagno and its impact on sediment geochemistry and vice versa. The findings reveal distinct redox gradients, microbial activities, and organic carbon remineralization processes in the deep sediment layers compared to the water column.
FRONTIERS IN EARTH SCIENCE
(2022)
Article
Ecology
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, Orit Sivan
Summary: Microbial communities in iron-rich methanic sediments of Lake Kinneret show phylogenetic and functional diversity, with key metabolic reactions being performed by archaea and bacteria, potentially involving electron transfer via transmembrane cytochromes and outer-membrane hexaheme c-type cytochrome (OmcS). Anaerobic oxidizers of methane and denitrifying methanotrophs may mediate anaerobic oxidation of methane (AOM) in these sediments, while potential aerobes also play a role in the oxidation of methane.
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
Biotechnology & Applied Microbiology
Tomohiro Watanabe, Kyoko Kubo, Yoshiharu Kamei, Hisaya Kojima, Manabu Fukui
Summary: Lake Harutori is a brackish meromictic lake with a steep gradient in shallow water. This study investigated the microbial community structure at different depths of the lake using 16S rRNA gene sequencing and CARD-FISH. The results revealed the presence of methanotrophic and sulfur-oxidizing bacteria populations, as well as methanogenic archaea in the deep water layer. Additionally, several uncultured bacterial groups were identified.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2022)
Article
Environmental Sciences
Ana Lucia Santoro, Alex Enrich-Prast, David Bastviken, Lars Tranvik, Camila Negrao Signori
Summary: Rates of dark inorganic carbon fixation (DCF) were highly variable among the studied lakes, with mostly production occurring below 10 mm of sediment in the anoxic zone. Although presenting a relatively low contribution in relation to BP and SOC, our study showed extensive microbial metabolism in the anaerobic sediment below the top centimeter, highlighting the importance of studying microbial processes across depth at fine scales.
Article
Biotechnology & Applied Microbiology
Jing Ding, Fan Qin, Changxin Li, Mingfang Tang, G. Daniel Sheng
Summary: The study examined the survival characteristics of DAMO microbes in Taihu Lake and found that DAMO bacteria and archaea displayed niche differentiation and different survival strategies. The abundance and association network of DAMO microbes varied among different nutrient regions, with DAMO bacteria acting as connectors in the mildly eutrophic region. The study expands our understanding of the ecological functions of DAMO microbes in freshwater environments.
ENVIRONMENTAL TECHNOLOGY & INNOVATION
(2022)
Article
Geosciences, Multidisciplinary
Xi Chen, Xianqiang Meng, Yinxian Song, Bin Zhang, Zhiwei Wan, Bingqing Zhou, Enlou Zhang
Summary: This study investigated the distribution of total organic carbon (TOC) and inorganic carbon (TIC) in Lake Qinghai, the largest saline lake in China. Results showed higher TOC content near human activities and lower in other areas, while TIC content increased towards the lake center, primarily depending on hydro-chemical and hydraulic characteristics. The inorganic carbon burial was approximately equal to organic carbon burial, suggesting that saline lakes contribute significantly to the global carbon budget.
FRONTIERS IN EARTH SCIENCE
(2021)
Article
Limnology
Sofia L. D'Ambrosio, Stephen M. Henderson, Jeffrey R. Nielson, John A. Harrison
Summary: Methane produced in anoxic sediments plays a significant role in the carbon economy of lakes and reservoirs. The physical and biogeochemical conditions in the bottom boundary layer influence the transport of methane from sediments to the lower layer of water. This study estimated methane fluxes across the bottom boundary layer of a eutrophic lake and found significant sub-daily and seasonal variability.
LIMNOLOGY AND OCEANOGRAPHY
(2022)
Article
Environmental Sciences
Josue Alegria-Gomez, Jose Humberto Castanon-Gonzalez, Juan Alfredo Hernandez-Garcia, Elizabeth Gonzalez-Terreros, Irving Oswaldo Velazquez-Rios, Victor Manuel Ruiz-Valdiviezo
Summary: In this study, the composition patterns of microbial communities in the vertical distribution of La Encantada lake in Mexico were explored, and their relationship with physicochemical properties of the water was investigated. The results showed that the composition of microbial communities varied with depth and physicochemical parameters, which could play a role as biological factors in the trophic states of the lake.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Microbiology
Timothy J. Williams, Michelle A. Allen, Jonathan F. Berengut, Ricardo Cavicchioli
Summary: Through genomic analysis, novel metabolic traits of Candidatus bacterial phyla Cloacimonadota and Omnitrophota have been identified, including carbon fixation using reverse tricarboxylic acid cycle, and strong biosynthetic capacity for organic compounds. Both taxa are inferred to form metabolic interactions with hydrogen-consuming partners in Ace Lake, occupying specific niches.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Limnology
Jose Luis Moreno, Jose Fernando Ortega, Miguel Angel Moreno, Rocio Ballesteros
Summary: High-resolution remote sensing imagery by unmanned aerial vehicles (UAVs) is a useful tool for assessing the ecological status of lakes and detecting important environmental events.
Article
Multidisciplinary Sciences
Till L. Bornemann, Panagiotis S. Adam, Victoria Turzynski, Ulrich Schreiber, Perla Abigail Figueroa-Gonzalez, Janina Rahlff, Daniel Koster, Torsten C. Schmidt, Ralf Schunk, Bernhard Krauthausen, Alexander J. Probst
Summary: The Earth's mantle releases CO2 and other gases to the atmosphere, shaping microbial metabolism at volcanic sites globally. However, little is known about the impact of mantle degassing on microbial life under non-thermal conditions. In this study, researchers compared microbial communities from a cold-water geyser with other deep subsurface sites, and found that an uncultivated archaeon played a key role. These findings suggest that subsurface ecosystems affected by geological degassing are important for microbial life in the deep biosphere.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Adrian Bozal-Leorri, Guntur Subbarao, Masahiro Kishii, Leyre Urmeneta, Victor Kommerell, Hannes Karwat, Hans-Joachim Braun, Pedro Ma Aparicio-Tejo, Ivan Ortiz-Monasterio, Carmen Gonzalez-Murua, Ma Begona Gonzalez-Moro
Summary: Synthetic nitrification inhibitors (SNI) and biological nitrification inhibitors (BNI) are promising tools to limit agricultural nitrogen pollution. Introducing the chromosome region (Lr#n-SA) controlling BNI production into wheat cultivars can enhance nitrogen uptake and utilization.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Engineering, Environmental
Maria Belen Sathicq, Raffaella Sabatino, Andrea Di Cesare, Ester M. Eckert, Diego Fontaneto, Michela Rogora, Gianluca Corno
Summary: This study investigated the impact of tyre wear microplastic particles (TWP) and polyethylene terephthalate (PET) particles on the microbial communities in water. The results showed that TWP acted as an additional carbon source, promoting the growth of potentially harmful bacteria, while PET provided a refuge for pathogens from wastewater effluent.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Engineering, Environmental
Raffaella Sabatino, Francesco Furia, Ester M. Eckert, Marco Minella, Gianluca Corno, Andrea Di Cesare, Davide Vione
Summary: The study found that the ZVI-Fenton process effectively reduces the total content of potentially pathogenic bacteria in wastewater, although its effect on decreasing live bacteria was comparable to H2O2 alone. However, it did not reduce the relative abundance of the tested antibiotic resistance genes or class 1 integrons.
JOURNAL OF WATER PROCESS ENGINEERING
(2022)
Article
Biodiversity Conservation
Wolfgang Sterrer, Martin Sorensen, Matteo Cecchetto, Alejandro Martinez, Raffaella Sabatino, Ester M. Eckert, Diego Fontaneto, Stefano Schiaparelli
Summary: This study reported the discovery of at least two species of the phylum Gnathostomulida in the Southern Ocean and along the shores of the Ross Sea in Antarctica for the first time, utilizing morphological inspection and DNA metabarcoding techniques for species identification.
Article
Marine & Freshwater Biology
Ester M. Eckert, Tommaso Cancellario, Paul L. E. Bodelier, Steven A. J. Declerck, Liang Diwen, Sainur Samad, Monika Winder, Libin Zhou, Diego Fontaneto
Summary: This study investigates the factors contributing to the differences in microbiomes associated with rotifers, and finds that host ecology and habitat have a stronger influence than host phylogenetic distances.
Article
Environmental Sciences
Raffaella Sabatino, Pedro J. Cabello-Yeves, Ester M. Eckert, Gianluca Corno, Cristiana Callieri, Diego Brambilla, Nina Dzhembekova, Snejana Moncheva, Andrea Di Cesare
Summary: Seas and oceans serve as a global reservoir of antibiotic resistance genes (ARGs). This study analyzed metagenomic data from the Black Sea and found that ARGs were more abundant in the deep water layers, with depth being the main driver of ARG and metal resistance gene (MRG) diversity. The integron integrase gene abundance and composition were not influenced by water depth and did not correlate with ARGs. Some of the obtained MAGs harbored intI gene along with multiple ARGs and MRGs, suggesting the presence of multidrug resistant bacteria and the involvement of MRGs and integrons in ARG selection.
ENVIRONMENTAL POLLUTION
(2022)
Article
Ecology
Karel Simek, Indranil Mukherjee, Tiberiu Szoke-Nagy, Markus Haber, Michaela M. Salcher, Rohit Ghai
Summary: Morphologically indistinguishable aplastidic cryptophytes were found to be ubiquitous and prominent protistan bacterivores in freshwater ecosystems, playing important roles in carbon flow. These heterotrophic cryptophytes were generally smaller and more abundant than their chloroplast-bearing counterparts, and their diversity has been largely undiscovered.
Article
Environmental Sciences
Marco De Carluccio, Raffaella Sabatino, Ester M. Eckert, Andrea Di Cesare, Gianluca Corno, Luigi Rizzo
Summary: The impact of Fenton oxidation (FO) and Air stripping (AS) pre-treatments on the bacterial community of a biological activated sludge (B-AS) process for the co-treatment of mature landfill leachate (MLL) and urban wastewater (UWW) was assessed. The combination of FO and AS allowed for successful operation of the B-AS and effective treatment of MLL, by improving biodegradability and reducing ammonia concentration. For bacterial community shifting, BOD5/COD was found to be the key factor. The results suggest that a suitable combination of pre-treatments can reduce the negative effect of MLL on the B-AS process and shorten the acclimatization time for autochthonous bacteria.
Review
Microbiology
Maria-Cecilia Chiriac, Markus Haber, Michaela M. Salcher
Summary: Pelagic microbes in lakes and oceans can be grouped into free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. This review identifies genomic traits that enable pelagic freshwater microbes to thrive in their habitat, by comparing the genetic differences between pelagic marine and freshwater microbes and also freshwater sediment microbes. Metabolic differences, including transport functions, environmental information processing, and electron transport chain components, are found in pelagic freshwater microbes. This review also discusses lineages and mechanisms involved in habitat transitions and describes the distribution, ecology, and genomic make-up of abundant freshwater prokaryotes.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Ester M. Eckert, Silvia Galafassi, Marcela Bastidas Navarro, Andrea Di Cesare, Gianluca Corno
Summary: Stochastic or deterministic processes control the assembly of bacterial communities in aquatic environments exposed to antibiotics. Microdiversity influences the stability of freshwater communities, causing rare taxa to become abundant when disturbance occurs. Disturbance by antibiotics increases the similarity between bacterial communities from different freshwater systems, but the similarity decreases when the antibiotic pressure is released. Antibiotics impact bacterial communities at both the cell and community level, altering phenotypes, genotypes, and bacterial interactions.
ENVIRONMENTAL POLLUTION
(2023)
Article
Environmental Sciences
Gianluca Corno, Timothy Ghaly, Raffaella Sabatino, Ester M. Eckert, Silvia Galafassi, Michael R. Gillings, Andrea Di Cesare
Summary: This study investigated the abundance of class 1 integrons and their associated antibiotic resistance genes (ARGs) in a freshwater system consisting of a lake-river-lake continuum. The results showed that class 1 integrons and their associated ARGs were more abundant in riverine sampling sites receiving treated wastewater. Moreover, high-risk ARGs, including genes encoding resistance to aminoglycosides, were correlated with class 1 integrons.
ENVIRONMENTAL POLLUTION
(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.
Article
Multidisciplinary Sciences
David Kamanda Ngugi, Michaela M. Salcher, Adrian-Stefan Andrei, Rohit Ghai, Franziska Klotz, Maria-Cecilia Chiriac, Danny Ionescu, Petra Buesing, Hans-Peter Grossart, Peng Xing, John C. Priscu, Salmor Alymkulov, Michael Pester
Summary: A study has found that the species diversity of ammonia-oxidizing archaea (AOA) in freshwater is lower compared to marine environments. The research also reveals that an uncultured freshwater AOA, Candidatus Nitrosopumilus limneticus, evolved in European lakes 13 million years ago and has remained genetically stable. These findings provide insights into the genetic diversity and adaptive mechanisms of AOA in lakes.
Article
Ecology
Vinicius. S. S. Kavagutti, Maria-Cecilia Chiriac, Rohit Ghai, Michaela. M. M. Salcher, Markus Haber
Summary: The low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' are abundant in freshwater environments globally and have high levels of microdiversity, possibly due to predation pressure by phages. In this study, a novel species of the genus 'Ca. Planktophila' was isolated and used to cultivate the first two phages infecting this bacterial order. These phages have unique genomes and exhibit high levels of horizontal gene transfer.
Article
Limnology
Giuseppe Garlasche, Giulia Borgomaneiro, Roberta Piscia, Marina Manca, Ester M. Eckert, Diego Fontaneto
Summary: Biodiversity surveys through morphology provide valuable data for biological monitoring, but the advent of metabarcoding and massive sequencing is seen as a potential advance. In this study of Lake Maggiore in Northern Italy, we tested whether metabarcoding can provide reliable results by using a detailed knowledge of local diversity, creating a reference library using DNA taxonomy, and developing custom primers. Our results show that occurrences from metabarcoding can be reliable, but read numbers from massive sequencing cannot be related to abundance. Metabarcoding data can be used to monitor species occurrence, but not abundance.
JOURNAL OF LIMNOLOGY
(2023)
Article
Marine & Freshwater Biology
Noemi Colinas, Javier Montero-Pau, Maria Jose Carmona, Raffaella Sabatino, Andrea Di Cesare, Ester Maria Eckert, Eduardo M. Garcia-Roger
Summary: A non-genetic transgenerational effect on sexual reproduction was observed in Brachionus plicatilis clones from more predictable environments, indicating a potential role of estradiol in this effect. However, the molecular basis of this effect is still unknown. The expression of the edh gene involved in estradiol synthesis increased across generations in clones from the more predictable ponds, but no differences were found in the meth gene.