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Microbial Ecology | Page 2

Christopher J Sedlacek, Brian McGowan, Yuichi Suwa, Luis Sayavedra-Soto, Hendrikus J Laanbroek, Lisa Y Stein, Jeanette M Norton, Martin G Klotz, Annette Bollmann
Ammonia-oxidizing bacteria (AOB) within the genus Nitrosomonas perform the first step in nitrification, ammonia oxidation, and are found in diverse aquatic and terrestrial environments. Nitrosomonas AOB were grouped into six defined clusters, which correlate with physiological characteristics that contribute to adaptations to a variety of abiotic environmental factors. A fundamental physiological trait differentiating Nitrosomonas AOB is the adaptation to either low (cluster 6a) or high (cluster 7) ammonium concentrations...
April 11, 2019: Microbial Ecology
Wei Wei, Nannan Wang, Lanlan Cai, Chuanlun Zhang, Nianzhi Jiao, Rui Zhang
Virioplankton is an important component of the aquatic ecosystem and plays multiple ecological and biogeochemical roles. Although the spatial and temporal distributions and dynamics of virioplankton have been well investigated in riverine and marine environments, little is known about the dynamics and environmental controlling mechanisms of virioplankton in estuaries. In this study, viral abundance, production and decay were examined in the Pearl River Estuary (PRE), one of the largest estuaries in China. The influences of freshwater and seawater mixing on viral ecological dynamics were evaluated with several cross-transplant experiments...
April 10, 2019: Microbial Ecology
G P Stamou, N Monokrousos, D Gwynn-Jones, D E Whitworth, E M Papatheodorou
Network analysis was used to show changes in network attributes by analyzing the relations among the main soil microbial groups in a potted tomato soil inoculated with arbuscular mycorrhizal fungus, treated with low doses of Mentha spicata essential oil, or both, and then exposed to tenfold higher oil addition (stress pulse). Pretreatments were chosen since they can induce changes in the composition of the microbial community. Cellular phospholipid fatty acids (PLFAs) and the activity of six soil enzymes, mainly involved in the N-cycle were measured...
April 5, 2019: Microbial Ecology
Jiangang Han, Shengyan Wang, Diwu Fan, Yanhui Guo, Chenglei Liu, Yongli Zhu
Hormetic dose-response that involved Cd in soils is increasingly paid attentions for risk assessment of Cd toxicity, but insufficient studies were conducted to define the temporary modification of soil enzyme and the potential microbial responses. The present study chooses soil alkaline phosphatase (ALP) as endpoint to uncover the time-dependent hormetic responses to low doses of Cd and its association with bacterial community composition. The results showed that addition of 0.01-3.0 mg kg-1 Cd significantly increased ALP's activities with maximum stimulatory magnitude of 11...
April 5, 2019: Microbial Ecology
Myra C Hughey, Eric R Sokol, Jenifer B Walke, Matthew H Becker, Lisa K Belden
Animals host a wide diversity of symbiotic microorganisms that contribute important functions to host health, and our knowledge of what drives variation in the composition of these complex communities continues to grow. Microbiome studies at larger spatial scales present opportunities to evaluate the contribution of large-scale factors to variation in the microbiome. We conducted a large-scale field study to assess variation in the bacterial symbiont communities on adult frog skin (Pseudacris crucifer), characterized using 16S rRNA gene amplicon sequencing...
April 4, 2019: Microbial Ecology
Shubin Lan, Andrew David Thomas, Stephen Tooth, Li Wu, Chunxiang Hu
In dryland regions, biological soil crusts (BSCs) have numerous important ecosystem functions. Crust species and functions are, however, highly spatially heterogeneous and remain poorly understood at a range of scales. In this study, chlorophyll fluorescence imaging was used to quantify millimeter-scale patterns in the distribution and activity of photosynthetic organisms in BSCs of different successional stages (including cyanobacterial, lichen, moss three main successional stages and three intermixed transitional stages) from the Tengger Desert, China...
April 4, 2019: Microbial Ecology
Renee Johansen, Michaeline Albright, La Verne Gallegos-Graves, Deanna Lopez, Andreas Runde, Thomas Yoshida, John Dunbar
The study of microbial community functions necessitates replicating microbial communities. Variation in community development over time renders this an imperfect process. Thus, anticipating the likely degree of variation among replicate communities may aid in experimental design. We examined divergence in replicate community composition and function among 128 naturally assembled starting communities obtained from soils, each replicated three times, following a 30-day microcosm incubation period. Bacterial and fungal communities diverged in both composition and function among replicates, but remained much more similar to each other than to communities from different starting inocula...
April 2, 2019: Microbial Ecology
Stephanie R Hogue, Maria F Gomez, Wildson Vieira da Silva, Christine M Pierce
Fecal specimen collection in the clinical setting is often unfeasible for large population studies, especially because cancer patients on immunotherapy often experience constipation. A method for constructing and using an at-home stool collection kit designed for epidemiological studies in cancer patients is presented. Participation and compliance rates of the collection kit among late-stage cancer patients from an ongoing, longitudinal study are also discussed. The kit includes three different media on which samples are introduced...
March 30, 2019: Microbial Ecology
Lucie Semenec, Ismael A Vergara, Andrew E Laloo, Elizabeth R Mathews, Philip L Bond, Ashley E Franks
The published version of this article contained an old version of Fig. 2.
March 30, 2019: Microbial Ecology
Cassidy L Klima, Devin B Holman, Brenda J Ralston, Kim Stanford, Rahat Zaheer, Trevor W Alexander, Tim A McAllister
Bovine respiratory disease (BRD) continues to be a serious health problem in beef cattle production. A multifactorial condition, BRD encompasses several types of pneumonia that are associated with multiple viral and bacterial agents. Comprehensive identification of microbes associated with BRD fatalities could enhance our understanding of the range of pathogens that contribute to the disease and identify new therapeutic targets. This study used metagenomic analysis to describe the lower respiratory tract microbiome and resistome of 15 feedlot cattle BRD and 3 non-BRD mortalities along with any affiliated integrative and conjugative elements (ICEs)...
March 27, 2019: Microbial Ecology
Michał Kolasa, Radosław Ścibior, Miłosz A Mazur, Daniel Kubisz, Katarzyna Dudek, Łukasz Kajtoch
Bacterial communities play a crucial role in the biology, ecology, and evolution of multicellular organisms. In this research, the microbiome of 24 selected beetle species representing five families (Carabidae, Staphylinidae, Curculionidae, Chrysomelidae, Scarabaeidae) and three trophic guilds (carnivorous, herbivorous, detrivorous) was examined using 16S rDNA sequencing on the Illumina platform. The aim of the study was to compare diversity within and among species on various levels of organization, including evaluation of the impact of endosymbiotic bacteria...
March 27, 2019: Microbial Ecology
Saraswoti Neupane, David Modry, Barbora Pafčo, Ludek Zurek
The original published version of this article had mistakes in figure legends. Correct figure legends are presented below.
March 26, 2019: Microbial Ecology
Yanshuo Pan, Yucheng Wu, Xuanzhen Li, Jun Zeng, Xiangui Lin
Selective inhibition (SI) has been routinely used to differentiate the contributions of bacteria and fungi to soil ecological processes. SI experiments typically measured rapid responses within hours since the addition of inhibitor, but the long-term effects of selective biocides on microbial community composition and function were largely unknown. In this study, a microcosm experiment was performed with an agricultural soil to explore the effectiveness of two bactericides (bronopol, streptomycin) and two fungicides (cycloheximide, captan), which were applied at two different concentrations (2 and 10 mg g-1 )...
March 25, 2019: Microbial Ecology
Keunje Yoo, Il Han, Kwan Soo Ko, Tae Kwon Lee, Hyunji Yoo, Muhammad Imran Khan, James M Tiedje, Joonhong Park
Asian dust (AD) events have received significant attention due to their adverse effects on ecosystems and human health. However, detailed information about airborne pathogens associated with AD events is limited. This study monitored airborne bacterial communities and identified AD-specific bacteria and the potential hazards associated with these bacteria during AD events. Over a 33-month period, 40 air samples were collected under normal atmospheric conditions (non-AD events; n = 34) and during AD events (n = 6)...
March 23, 2019: Microbial Ecology
Jiajie Hu, Shuai Liu, Weiling Yang, Zhanfei He, Jiaqi Wang, Huan Liu, Ping Zheng, Chuanwu Xi, Fang Ma, Baolan Hu
The intertidal zone is an important buffer and a nitrogen sink between land and sea. Ammonia oxidation is the rate-limiting step of nitrification, conducted by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, it remains a debatable issue regarding dominant ammonia oxidizers in this region, and environmental factors driving their spatiotemporal niche differentiation have yet to be identified. In this study, intertidal and subtidal zones of Zhoushan Islands were selected for seasonal sampling...
March 22, 2019: Microbial Ecology
Mathilde Borg Dahl, Asker Daniel Brejnrod, Jakob Russel, Søren Johannes Sørensen, Martin Schnittler
We used direct DNA amplification from soil extracts to analyze microbial communities from an elevational transect in the German Alps by parallel metabarcoding of bacteria (16S rRNA), fungi (ITS2), and myxomycetes (18S rRNA). For the three microbial groups, 5710, 6133, and 261 operational taxonomic units (OTU) were found. For the latter group, we can relate OTUs to barcodes from fruit bodies sampled over a 4-year period. The alpha diversity of myxomycetes was positively correlated with that of bacteria. Vegetation type was found to be the main explanatory parameter for the community composition of all three groups and a substantial species turnover with elevation was observed...
March 22, 2019: Microbial Ecology
Jérémy Jabiol, Antoine Lecerf, Sylvain Lamothe, Mark O Gessner, Eric Chauvet
Rates of leaf litter decomposition in streams are strongly influenced both by inorganic nutrients dissolved in stream water and by litter traits such as lignin, nitrogen (N) and phosphorus (P) concentrations. As a result, decomposition rates of different leaf species can show contrasting responses to stream nutrient enrichment resulting from human activities. It is unclear, however, whether the root cause of such discrepancies in field observations is the interspecific variation in either litter nutrient or litter lignin concentrations...
March 21, 2019: Microbial Ecology
Josef Hýsek, Radek Vavera, Pavel Růžek
In field and laboratory experiments during 2014-2017, we investigated the influence of lower and higher cultivation intensity of wheat and ecological factors (weather-temperature and rainfalls, year) on the occurrence of phytopathogenic fungi on the leaves of winter wheat. The prevailing fungi in those years were Mycosphaerella graminicola (Fuckel) J. Schrott and Pyrenophora tritici-repentis (Died.) Drechsler. Using cluster analysis, we statistically evaluated interrelationships of known factors on the abundance of the fungi on leaf surfaces...
March 21, 2019: Microbial Ecology
Susan Cockerham, Becky Lee, Rachael A Orben, Robert M Suryan, Leigh G Torres, Pete Warzybok, Russell Bradley, Jaime Jahncke, Hillary S Young, Cleber Ouverney, Scott A Shaffer
Avian species host diverse communities of microorganisms which have important roles in the life of birds, including increased metabolism, protection from disease, and immune system development. Along with high human populations and a diversity of human uses of coastal zones, anthropogenic food sources are becoming increasingly available to some species, including gulls. Anthropogenic associations increase the likelihood of encountering foreign or pathogenic bacteria. Diseases in birds caused by bacteria are a substantial source of avian mortality; therefore, it is essential to characterize the microbiome of seabirds...
March 20, 2019: Microbial Ecology
Shawn P Brown, Ari Jumpponen
Snows that persist late into the growing season become colonized with numerous metabolically active microorganisms, yet underlying mechanisms of community assembly and dispersal remain poorly known. We investigated (Illumina MiSeq) snow-borne bacterial, fungal, and algal communities across a latitudinal gradient in Fennoscandia and inter-continental distribution between northern Europe and North America. Our data indicate that bacterial communities are ubiquitous regionally (across Fennoscandia), whereas fungal communities are regionally heterogeneous...
March 13, 2019: Microbial Ecology
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