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FEMS Microbiology Ecology

Josh Faber-Hammond, Kaitlin P Coyle, Shannon K Bacheller, Cameron G Roberts, Jay Mellies, Reade B Roberts, Suzy C P Renn
Many of the various parental care strategies displayed by animals are accompanied by a significant reduction in food intake that imposes substantial energy trade-offs. Mouthbrooding, as seen in several species of fish in which the parent holds the developing eggs and fry in the buccal cavity, represents an extreme example of reduced food intake during parental investment and is accompanied by a range of physiological adaptations. In this study we use 16S sequencing to characterize the gut microbiota of female A...
February 11, 2019: FEMS Microbiology Ecology
Doris Y W Di, Hansub Shin, Dukki Han, Tatsuya Unno, Hor-Gil Hur
A horizontal, fluorophore-enhanced, repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique (HFERP) was adapted to examine the genotypic richness and source differentiation of Vibrio parahaemolyticus (n = 1,749) isolated from tidal water and mud of southern coast of South Korea. The number of unique genotypes observed from June (163, 51.9%), September (307, 63.9%), December (205, 73.8%), and February (136, 74.7%), indicating a high degree of genetic diversity. Contrary, lower genetic diversity was detected in April (99, 46...
February 7, 2019: FEMS Microbiology Ecology
Achouak Wafa, Danis Abrouk, Julien Guyonnet, Mohamed Barakat, Philippe Ortet, Laurent Simon, Catherine Lerondelle, Thierry Heulin, Feth El Zahar Haichar
In the rhizosphere, complex and dynamic interactions occur between plants and microbial networks that are primarily mediated by root exudation. Plants exude various metabolites that may influence the rhizosphere microbiota. However, few studies have sought to understand the role of root exudation in shaping the functional capacities of the microbiota. In this study, we aim to determine the impact of plants on the diversity of active microbiota and their ability to denitrify via root exudates. For that purpose, we grew four plant species, Triticum aestivum, Brassica napus, Medicago truncatula and Arabidopsis thaliana, separately in the same soil...
February 6, 2019: FEMS Microbiology Ecology
Dennis Goss-Souza, Lucas William Mendes, Clovis Daniel Borges, Jorge L M Rodrigues, Siu Mui Tsai
The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due liming and fertilization in long-term no-till cropping...
February 1, 2019: FEMS Microbiology Ecology
Carla Cruz-Paredes, Nanna B Svenningsen, Ole Nybroe, Rasmus Kjøller, Tobias Guldberg Frøslev, Iver Jakobsen
Most plants form symbiotic associations with arbuscular mycorrhizal fungi (AMF). AMF increase the uptake of plant nutrients by extending their extra-radical mycelium (ERM) in the soil where other groups of microorganisms may suppress the activity of the ERM. However, little is known about such suppression in natural soils. This work aimed to investigate the incidence of AMF suppression among soils sampled from highly variable natural ecosystems, and used 33P uptake by the ERM to evaluate AMF activity. A second aim was to identify factors behind the observed AMF-suppression...
February 1, 2019: FEMS Microbiology Ecology
Sean M McAllister, Ryan M Moore, Amy Gartman, George W Luther, David Emerson, Clara S Chan
The Zetaproteobacteria are a class of bacteria typically associated with marine Fe(II)-oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe(II) oxidation. In addition to deep sea and shallow hydrothermal vents, Zetaproteobacteria are found in coastal sediments, other marine subsurface environments, steel corrosion biofilms, and saline terrestrial springs. Isolates from a range of environments all grow by autotrophic Fe(II) oxidation...
January 30, 2019: FEMS Microbiology Ecology
Shao-Song Wu, Marcela Hernández, Yong-Cui Deng, Cheng Han, Xin Hong, Jie Xu, Wen-Hui Zhong, Huan Deng
Previous studies showed that exoelectrogenic bacteria in paddy soil could suppress methanogens and methanogenesis after they were enriched by application of Fe3+ or running microbial fuel cells (MFCs). However, it is unknown the relationship between exoelectrogenic bacteria and methanogens without the enrichment process. Our study was conducted in three rice paddy fields in China and over three seasons. We explored novel MFC based sensors to in situ detect voltage signals that were generated from paddy soil within ten minutes...
January 30, 2019: FEMS Microbiology Ecology
Qiang Zheng, Jiayao Lu, Yu Wang, Nianzhi Jiao
Interactions between photoautotrophs and heterotrophs are central to marine microbial ecosystems. Synechococcus are dominant marine phototrophs, and they are frequently associated with heterotrophic bacteria. These co-cultures provide a useful research system to investigate photoautotroph-heterotroph interactions in marine systems. Bacteria within the Roseobacter clade and Flavobacteria are two of the main bacterial lineages that exhibit intimate associations with Synechococcus populations. We conducted metagenomic analyses of a Synechococcus culture, followed by genomic binning of metagenomic contigs, and recovered five nearly complete genomes, including members of the Roseobacter clade (i...
January 28, 2019: FEMS Microbiology Ecology
Kristin Steger, Amy Taeyen Kim, Lars Ganzert, Hans-Peter Grossart, David R Smart
We studied bacterial abundance and community structure of five soil cores using high-throughput sequencing of the 16S rRNA gene. Shifts in the soil bacterial composition were more pronounced within a vertical profile than across the landscape. Soil organic carbon (SOC) and nitrogen (N) concentrations decreased exponentially with soil depth and revealed a buried carbon-rich horizon between 0.8 and 1.3 m across all soil cores. This buried horizon was phylogenetically similar to its surrounding subsoils supporting the idea that the type of carbon, not necessarily the amount of carbon was driving the apparent similarities...
January 24, 2019: FEMS Microbiology Ecology
Samantha Fernández-Brime, Lucia Muggia, Stefanie Maier, Martin Grube, Mats Wedin
Borderline lichens are simple mutualistic symbioses between fungi and algae, where the fungi form loose mycelia interweaving algal cells, instead of forming a lichen thallus. Schizoxylon albescens shows two nutritional modes: it can either live as a borderline lichen on Populus tremula bark or as a saprotroph on Populus wood. This enables us to investigate the microbiota diversity in simple fungal-algal associations and to study the impact of lichenization on the structure of bacterial communities. We sampled three areas in Sweden covering the distribution of Schizoxylon, and using high-throughput sequencing of the 16S rRNA gene and fluorescence in situ hybridization we characterized the associated microbiota...
January 22, 2019: FEMS Microbiology Ecology
Jiapeng Wu, Yiguo Hong, Xiangyang Chang, Lijing Jiao, Yiben Li, Xiaohan Liu, Haitao Xie, Ji-Dong Gu
Ca. Scalindua is an exclusive genus of anammox bacteria known to exhibit low diversity found in deep-sea ecosystems. In this study, the community composition of anammox bacteria in surface sediments of the South China Sea (SCS) was analyzed using high-throughput sequencing techniques. Results indicated that the dominant OTUs were related to three different genera of anammox bacteria, identified as Ca. Scalindua (87.29%), Ca. Brocadia (10.27%) and Ca. Kuenenia (2.44%), in order of decreasing abundance. Quantitative PCR analysis of anammox-specific 16S rRNA and hzsB genes confirmed that the abundance of anammox bacteria in deep-sea surface sediments ranged from 4...
January 22, 2019: FEMS Microbiology Ecology
Piaszczyk Wojciech, Blonska Ewa, Lasota Jaroslaw
Despite the increasing number of studies on deadwood, we still have limited knowledge of its dynamics. The aim of this study was to examine the effect of deadwood on the biochemical properties of soil and stabilization of soil organic matter (SOM). The investigation was carried out in the Czarna Rózga Reserve in Central Poland. The logs of four tree species at different stages of decomposition (III, IV and V) were selected for the analysis. Three replicate logs were sampled for each combination of decay classes, and the soil samples were collected from directly under the logs and from 1 m away from the logs...
January 21, 2019: FEMS Microbiology Ecology
Wiebke Sickel, Anna-Lena Van de Weyer, Felix Bemm, Jörg Schultz, Alexander Keller
The carnivorous Venus flytrap (Dionaea muscipula) overcomes environmental nutrient limitation by capturing small animals. Such prey is digested with an acidic enzyme-containing mucilage that is secreted into the closed trap. Surprisingly little is known about associations with microorganisms, though. Therefore, we assessed microbiota of traps and petioles for the Venus flytrap by 16S amplicon meta-barcoding. We further performed time-series assessments of dynamics during digestion in traps and experimental acidification of petioles...
January 16, 2019: FEMS Microbiology Ecology
Chyrene Moncada, Christiane Hassenrück, Astrid Gärdes, Cecilia Conaco
Marine aquaculture is a major industry that supports the economy in many countries, including the Philippines. However, excess feeds and fish waste generated by mariculture activities contribute an immense nutrient load to the environment that can affect the underlying sediment. To better understand these impacts, we compared the physicochemical characteristics and microbial community composition of sediments taken at a fish cage and an off cage site in Bolinao, Philippines. Sediments and pore water at the fish cage site showed evidence of greater organic enrichment relative to the off cage site...
January 14, 2019: FEMS Microbiology Ecology
Michael A Carson, Suzanna Bräuer, Nathan Basiliko
Methanogens are among the oldest forms of life on Earth and are detectable in a wide range of environments, but our knowledge of their overall diversity and functioning is limited. Peatlands in particular host a broad range of methanogens that contribute large amounts of methane to the atmosphere, but are largely underrepresented in pure cultures. Here we anaerobically enriched peat with common growth substrates, supplements, and antibiotics to identifying novel methanogen sequences and potential growth conditions...
January 14, 2019: FEMS Microbiology Ecology
Frederik Bak, Ole Nybroe, Bangxiao Zheng, Nora Badawi, Xiuli Hao, Mette Haubjerg Nicolaisen, Jens Aamand
Preferential flow paths in subsurface soils serve as transport routes for water, dissolved organic matter and oxygen. Little is known about bacterial communities in flow paths or in subsoils below about four metres. We compared communities from preferential flow paths (biopores, fractures and sand lenses) with those in adjacent matrix sediments of clayey till from the plough layer to a depth of six metres. 16S rRNA gene-targeted community analysis showed bacterial communities of greater abundance and diversity in flow paths than in matrix sediments at all depths...
January 11, 2019: FEMS Microbiology Ecology
Rok Kostanjšek, Ylenia Prodan, Blaž Stres, Peter Trontelj
The European cave salamander Proteus anguinus is a charismatic amphibian endemic to the concealed and inaccessible subterranean waters of the Dinaric Karst. Despite its exceptional conservation importance not much is known about its ecology and interactions with the groundwater microbiome. The cutaneous microbiota of amphibians is an important driver of metabolic capabilities and immunity, and thus a key factor of their wellbeing and survival. We used high-throughput 16S rRNA gene sequencing based on seven variable regions to examine the bacteriome of the skin of five distinct evolutionary lineages of P...
January 11, 2019: FEMS Microbiology Ecology
William J Landesman, Zachary B Freedman, David M Nelson
The temporal dynamics of soil bacterial communities are understudied, but such understanding is critical to elucidating the drivers of community variation. The goal of this study was to characterize how soil bacterial communities vary across diurnal, sub-seasonal and seasonal time-scales in a 5.8 m2 plot and test the hypothesis that bacterial diversity varies on each of these scales. We used 16S rDNA gene amplicon sequencing to quantify the alpha and beta diversity of soil bacteria as well as the Net Relatedness Index and Nearest Taxon Indices to assess the degree of phylogenetic clustering, and the extent to which community shifts were driven by stochastic vs...
January 9, 2019: FEMS Microbiology Ecology
Congcong Shen, Yu Shi, Kunkun Fan, Jin-Sheng He, Jonathan M Adams, Yuan Ge, Haiyan Chu
Although studies of elevational diversity gradient for microbes have attracted considerable attention, the generality of these patterns and their underlying drivers are still poorly understood. Here, we investigated bacterial distribution across a high elevational gradient (4328 m - 5228 m a.s.l.) along the Nyainqêntanglha mountains on the Southwestern Tibetan Plateau. We found a decreasing diversity trend with increasing elevation, with pH contributing most to the diversity variation, followed by elevation and mean annual temperature (MAT)...
January 9, 2019: FEMS Microbiology Ecology
Petr Baldrian
The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions...
January 9, 2019: FEMS Microbiology Ecology
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