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Microbial Ecology

Alison A Bockoven, Elizabeth C Bondy, Matthew J Flores, Suzanne E Kelly, Alison M Ravenscraft, Martha S Hunter
Facultative, intracellular bacterial symbionts of arthropods may dramatically affect host biology and reproduction. The length of these symbiont-host associations may be thousands to millions of years, and while symbiont loss is predicted, there have been very few observations of a decline of symbiont infection rates. In a population of the sweet potato whitefly species (Bemisia tabaci MEAM1) in Arizona, USA, we documented the frequency decline of a strain of Rickettsia in the Rickettsia bellii clade from near-fixation in 2011 to 36% of whiteflies infected in 2017...
August 12, 2019: Microbial Ecology
Logan Gray, Gavin Kernaghan
Ectomycorrhizal (ECM) fine roots account for a substantial proportion of forest production and their decomposition releases large amounts of nutrients to the soil ecosystem. However, little is known about the fungi involved in ECM decomposition, including assemblages of fungal saprotrophs, endophytes, and the ECM fungi themselves. To follow fungal succession during the degradation of senescing fine roots, understory seedlings of Abies balsamea and Picea rubens at two sites in the Acadian forest of Nova Scotia were either severed at the root collar or left as controls...
August 8, 2019: Microbial Ecology
Joseph A Moss, Nine L Henriksson, J Dean Pakulski, Richard A Snyder, Wade H Jeffrey
A latitudinal biodiversity gradient has captivated ecologists for years, and has become a widely recognized pattern in biogeography, manifest as an increase in biodiversity from the poles to the tropics. Oceanographers have attempted to discern whether these distribution patterns are shared with marine biota, and a lively debate has emerged concerning the global distribution of microbes. Limitations in sampling resolution for such large-scale assessments have often prohibited definitive conclusions. We evaluated microbial planktonic communities along a ~ 15,400-km Pacific Ocean transect with DNA from samples acquired every 2 degrees of latitude within a 3-month period between late August and early November 2003...
August 7, 2019: Microbial Ecology
Mahbubul H Siddiqee, Rebekah Henry, Ana Deletic, Dieter M Bulach, Rhys A Coleman, David T McCarthy
Faecal contamination poses health risks for the recreational users of urban estuaries. However, our understanding of the potential pathogenicity of faecal microbes in these environments is limited. To this end, a study was conducted to understand the spatial and seasonal distribution of Salmonella in water and sediments of the Yarra River estuary, Melbourne, Australia. Among 210 samples in total, culturable Salmonella were recovered from 27%, 17%, and 19% of water, bank, and bed sediment samples, respectively...
August 5, 2019: Microbial Ecology
Jonas Frankel-Bricker, Michael J Song, Maia J Benner, Sarah Schaack
Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism's biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D...
August 3, 2019: Microbial Ecology
Mark T L Bonner, Diane E Allen, Richard Brackin, Tim E Smith, Tom Lewis, Luke P Shoo, Susanne Schmidt
Widespread and continuing losses of tropical old-growth forests imperil global biodiversity and alter global carbon (C) cycling. Soil organic carbon (SOC) typically declines with land use change from old-growth forest, but the underlying mechanisms are poorly understood. Ecological restoration plantations offer an established means of restoring aboveground biomass, structure and diversity of forests, but their capacity to recover the soil microbial community and SOC is unknown due to limited empirical data and consensus on the mechanisms of SOC formation...
August 1, 2019: Microbial Ecology
Barbara Cania, Gisle Vestergaard, Susanne Kublik, John Maximilian Köhne, Thomas Fischer, Andreas Albert, Barbro Winkler, Michael Schloter, Stefanie Schulz
Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as "glue" for soil particles. However, little is known about the dynamics of "soil glue" producers during the initial development of biocrusts...
August 1, 2019: Microbial Ecology
Antonio Cellini, Irene Donati, Luca Fiorentini, Elodie Vandelle, Annalisa Polverari, Vittorio Venturi, Giampaolo Buriani, Joel L Vanneste, Francesco Spinelli
The phyllosphere is a complex environment where microbes communicate through signalling molecules in a system, generally known as quorum sensing (QS). One of the most common QS systems in Gram-negative proteobacteria is based on the production of N-acyl homoserine lactones (AHLs) by a LuxI synthase and their perception by a LuxR sensor. Pseudomonas syringae pv. actinidiae (Psa), the aetiological agent of the bacterial canker of kiwifruit, colonises plant phyllosphere before penetrating via wounds and natural openings...
July 29, 2019: Microbial Ecology
Prabhat N Jha, Abu-Bakr Gomaa, Youssef G Yanni, Abd-Elgawad Y El-Saadany, Tiffany M Stedtfeld, Robert D Stedtfeld, Stephan Gantner, Benli Chai, James Cole, Syed A Hashsham, Frank B Dazzo
We examined the bacterial endophyte-enriched root-associated microbiome within rice (Oryza sativa) 55 days after growth in soil with and without urea fertilizer and/or biofertilization with a growth-promotive bacterial strain (Rhizobium leguminosarum bv. trifolii E11). After treatment to deplete rhizosphere/rhizoplane communities, washed roots were macerated and their endophyte-enriched communities were analyzed by 16S ribosomal DNA 454 amplicon pyrosequencing. This analysis clustered 99,990 valid sequence reads into 1105 operational taxonomic units (OTUs) with 97% sequence identity, 133 of which represented a consolidated core assemblage representing 12...
July 25, 2019: Microbial Ecology
Xi-En Long, Huaiying Yao
Rice root-associated microbial community play an important role in plant nutrient acquisition, biomass production, and stress tolerance. Herein, root-associated community assembly was investigated under different phosphate input levels in phosphorus (P)-deficient paddy soil. Rice was grown in a long-term P-depleted paddy soil with 0 (P0), 50 (PL), or 200 (PH) mg P2 O5 kg-1 application. DNA from root endophytes was isolated after 46 days, and PCR amplicons from archaea, bacteria, and fungi were sequenced by an Illumina Miseq PE300 platform, respectively...
July 24, 2019: Microbial Ecology
Joy L Shih, Karen E Selph, Christopher B Wall, Natalie J Wallsgrove, Michael P Lesser, Brian N Popp
Many sponges host abundant and active microbial communities that may play a role in the uptake of dissolved organic matter (DOM) by the sponge holobiont, although the mechanism of DOM uptake and metabolism is uncertain. Bulk and compound-specific isotopic analysis of whole sponge, isolated sponge cells, and isolated symbiotic microbial cells of the shallow water tropical Pacific sponge Mycale grandis were used to elucidate the trophic relationships between the host sponge and its associated microbial community...
July 17, 2019: Microbial Ecology
Jennifer A White, Alexander Styer, Laura C Rosenwald, Meghan M Curry, Kelton D Welch, Kacie J Athey, Eric G Chapman
Maternally inherited bacterial endosymbionts are common in arthropods, but their distribution and prevalence are poorly characterized in many host taxa. Initial surveys have suggested that vertically transmitted symbionts may be particularly common in spiders (Araneae). Here, we used diagnostic PCR and high-throughput sequencing to evaluate symbiont infection in 267 individual spiders representing 14 species (3 families) of agricultural spiders. We found 27 operational taxonomic units (OTUs) that are likely endosymbiotic, including multiple strains of Wolbachia, Rickettsia, and Cardinium, which are all vertically transmitted and frequently associated with reproductive manipulation of arthropod hosts...
July 12, 2019: Microbial Ecology
Pilar Eliana Puentes-Téllez, Joana Falcao Salles
Microorganisms play a crucial role in lignocellulosic degradation. Many enriched microbial communities have demonstrated to reach functional and structural stability with effective degrading capacities of industrial interest. These microbial communities are typically composed by only few dominant species and a high number of usually overlooked rare species. Here, we used two sources of lignocellulose (sugarcane bagasse and straw) in order to obtain lignocellulose-degrading bacteria through an enriched process, followed the selective trajectory of both abundant and rare bacterial communities by 16S rRNA gene amplification and analyzed the outcomes of selection in terms of capacities and specialization...
July 8, 2019: Microbial Ecology
Nick A Cutler, María Arróniz-Crespo, Lorna E Street, David L Jones, Dominique L Chaput, Thomas H DeLuca
The original version of this article contained an error in the Molecular Analysis subsection of the Methods.
July 8, 2019: Microbial Ecology
Hongyu Chen, Chunqing Li, Tao Liu, Shanyuan Chen, Heng Xiao
Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish...
July 6, 2019: Microbial Ecology
Dorsaf Kerfahi, Matthew Chidozie Ogwu, Dagvatseren Ariunzaya, Altantsetseg Balt, Dulamsuren Davaasuren, Orsoo Enkhmandal, Tsolmonjav Purevsuren, Amgaa Batbaatar, Mark Tibbett, Sainbileg Undrakhbold, Bazartseren Boldgiv, Jonathan M Adams
The soil fungal ecology of the southern Gobi region of Mongolia has been little studied. We utilized the ITS1 region from soil DNA to study possible influences soil metal concentrations on soil fungal community variation. In the sample network, a distinctive fungal community was closely associated with high zinc (Zn), lead (Pb), and copper (Cu) concentrations. The pattern of occurrence suggests that high metal concentrations are natural and not a product of mining activities. The metal-associated fungal community differs little from the "normal" community in its major OTUs, and in terms of major fungal guilds and taxa, and its distinctiveness depends on a combination of many less common OTUs...
July 4, 2019: Microbial Ecology
Erinne Stirling, Lynne M Macdonald, Ronald J Smernik, Timothy R Cavagnaro
Post-fire litter layers are composed of leaves and woody debris that predominantly fall during or soon after the fire event. These layers are distinctly different to pre-fire litters due to their common origin and deposition time. However, heterogeneity can arise from the variable thermal conditions in the canopy during fire. Therefore, in this study, we used thermally altered pine needles (heated to 40 °C, 150 °C, 260 °C and 320 °C for 1 h) in a laboratory incubation study for 43 days. These samples were measured for respiration throughout and extracted for DNA at the experiment's end; soil ribosomal RNA was analysed using Illumina sequencing (16S and internal transcribed spacer amplicons)...
July 2, 2019: Microbial Ecology
Linjian Ou, Xianling Qin, Xiaoyong Shi, Qingliang Feng, Shuwen Zhang, Songhui Lu, Yuzao Qi
Harmful blooms of Prorocentrum donghaiense occur annually in the phosphorus-scarce coastal waters of the East China Sea (ECS). The enzymatic activities of alkaline phosphatase (AP) and its regulation by external phosphorus were studied during a P. donghaiense bloom in this area. The AP characteristics of P. donghaiense was further compared with Prorocentrum minimum and Prorocentrum micans in monocultures with both bulk and single-cell enzyme-labeled fluorescence AP assays. Concentrations of dissolved inorganic phosphorus (DIP) varied between 0...
July 2, 2019: Microbial Ecology
Yue Yi, HuiZhong Wang, YaTing Chen, Min Gou, ZiYuan Xia, Bin Hu, Yong Nie, YueQin Tang
Butyrate is one of the most important intermediates during anaerobic digestion of protein wastewater, and its oxidization is considered as a rate-limiting step during methane production. However, information on syntrophic butyrate-oxidizing bacteria (SBOB) is limited due to the difficulty in isolation of pure cultures. In this study, two anaerobic chemostats fed with butyrate as the sole carbon source were operated at different dilution rates (0.01/day and 0.05/day). Butyrate- and acetate-oxidizing bacteria in both chemostats were investigated, combining DNA-Stable Isotope Probing (DNA-SIP) and 16S rRNA gene high-throughput sequencing...
July 1, 2019: Microbial Ecology
Dennis Goss-Souza, Lucas William Mendes, Jorge Luiz Mazza Rodrigues, Siu Mui Tsai
Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon...
June 27, 2019: Microbial Ecology
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