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- Author:
- Souffreau, Caroline; Busschaert, Pieter; Denis, Carla; Van Wichelen, Jeroen; Lievens, Bart; Vyverman, Wim; De Meester, Luc
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1271-1282
- ISSN:
- 1462-2912
- Subject:
- Nuphar; Phragmites; bacterioplankton; biofilm; community structure; environmental factors; microhabitats; ponds; species diversity
- Abstract:
- ... It is unknown whether bacterioplankton and biofilm communities are structured by the same ecological processes, and whether they influence each other through continuous dispersal (known as mass effects). Using a hierarchical sampling approach we compared the relative importance of ecological processes structuring the dominant fraction (relative abundance ≥0.1%) of bacterioplankton and biofilm comm ...
- DOI:
- 10.1111/1462-2920.14073
-
http://dx.doi.org/10.1111/1462-2920.14073
- Author:
- Chen, Annie I.; Goulian, Mark
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1283-1295
- ISSN:
- 1462-2912
- Subject:
- Escherichia coli; bacteria; disease transmission; genomic libraries; plasmids; stress response; transcription factors; water activity
- Abstract:
- ... The ability to survive conditions of low water activity is critical for the survival of many bacteria in the environment and facilitates disease transmission through food and contaminated surfaces. However, the molecular mechanisms that enable bacteria to withstand this condition remain poorly understood. Here we describe a network of regulators in Escherichia coli that are important for this bact ...
- DOI:
- 10.1111/1462-2920.14074
- PubMed:
- 29457688
- PubMed Central:
- PMC5869162
-
http://dx.doi.org/10.1111/1462-2920.14074
- Author:
- Troselj, Vera; Cao, Pengbo; Wall, Daniel
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 923-933
- ISSN:
- 1462-2912
- Subject:
- bacteria; genotype; phenotype; receptors; social networks; stochastic processes
- Abstract:
- ... The ability to recognize self and to recognize partnering cells allows microorganisms to build social networks that perform functions beyond the capabilities of the individual. In bacteria, recognition typically involves genetic determinants that provide cell surface receptors or diffusible signalling chemicals to identify proximal cells at the molecular level that can participate in cooperative p ...
- DOI:
- 10.1111/1462-2920.14005
- PubMed:
- 29194914
- PubMed Central:
- PMC5874169
-
http://dx.doi.org/10.1111/1462-2920.14005
- Author:
- Michalik, Anna; Schulz, Frederik; Michalik, Katarzyna; Wascher, Florian; Horn, Matthias; Szklarzewicz, Teresa
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1148-1157
- ISSN:
- 1462-2912
- Subject:
- Arsenophonus; Eriococcidae; bacteria; cytoplasm; histology; hosts; neck; nutrients; polyphyly; ribosomal RNA; scale insects; symbionts
- Abstract:
- ... Scale insects are commonly associated with obligate, intracellular microorganisms which play important roles in complementing their hosts with essential nutrients. Here we characterized the symbiotic system of Greenisca brachypodii, a member of the family Eriococcidae. Histological and ultrastructural analyses have indicated that G. brachypodii is stably associated with coccoid and rod‐shaped bact ...
- DOI:
- 10.1111/1462-2920.14057
-
http://dx.doi.org/10.1111/1462-2920.14057
- Author:
- Fowler, Susan Jane; Palomo, Alejandro; Dechesne, Arnaud; Mines, Paul D.; Smets, Barth F.
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1002-1015
- ISSN:
- 1462-2912
- Subject:
- Nitrosomonadaceae; ammonia; ammonium; bacterial communities; groundwater; nitrification; nitrifying bacteria; nitrogen content; nitrogen cycle; pollution load; sulfates; temperature; water microbiology
- Abstract:
- ... The recent discovery of completely nitrifying Nitrospira demands a re‐examination of nitrifying environments to evaluate their contribution to nitrogen cycling. To approach this challenge, tools are needed to detect and quantify comammox Nitrospira. We present primers for the simultaneous quantification and diversity assessement of both comammox Nitrospira clades. The primers cover a wide range of ...
- DOI:
- 10.1111/1462-2920.14033
-
http://dx.doi.org/10.1111/1462-2920.14033
- Author:
- Bell, Emma; Blake, Lynsay I.; Sherry, Angela; Head, Ian M.; Hubert, Casey R.J.
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1134-1147
- ISSN:
- 1462-2912
- Subject:
- ambient temperature; biogeography; biosphere; endospores; estuaries; habitats; industrial effluents; marine sediments; microbial communities; models; mutation; rivers; runoff; thermophilic bacteria
- Abstract:
- ... Endospores of thermophilic bacteria are found in cold and temperate sediments where they persist in a dormant state. As inactive endospores that cannot grow at the low ambient temperatures, they are akin to tracer particles in cold sediments, unaffected by factors normally governing microbial biogeography (e.g., selection, drift, mutation). This makes thermophilic endospores ideal model organisms ...
- DOI:
- 10.1111/1462-2920.14056
- PubMed:
- 29393553
- PubMed Central:
- PMC6849807
-
http://dx.doi.org/10.1111/1462-2920.14056
- Author:
- Katariya, Lakshya; Ramesh, Priya B.; Borges, Renee M.
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 971-979
- ISSN:
- 1462-2912
- Subject:
- Odontotermes obesus; Xylaria; carbon dioxide; ecosystem engineers; environmental factors; fungi; fungus gardening; microbial growth; microclimate; relative humidity; temperature; termite mounds
- Abstract:
- ... This study investigated for the first time the impact of the internal mound environment of fungus‐growing termites on the growth of fungal crop parasites. Mounds of the termite Odontotermes obesus acted as (i) temperature and relative humidity (RH) ‘stabilisers’ showing dampened daily variation and (ii) ‘extreme environments’ exhibiting elevated RH and CO₂ levels, compared to the outside. Yet, int ...
- DOI:
- 10.1111/1462-2920.14026
-
http://dx.doi.org/10.1111/1462-2920.14026
- Author:
- Espinosa, Javier; Labella, José I.; Cantos, Raquel; Contreras, Asunción
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1240-1252
- ISSN:
- 1462-2912
- Subject:
- Cyanobacteria; adenosine diphosphate; adenosine triphosphate; autotrophs; carbon; energy; nitrogen; photosynthesis; proteins; signal transduction
- Abstract:
- ... Cyanobacteria, phototrophic organisms performing oxygenic photosynthesis, must adapt their metabolic processes to the challenges imposed by the succession of days and nights. Two conserved cyanobacterial proteins, PII and PipX, function as hubs of the nitrogen interaction network, forming complexes with a variety of diverse targets. While PII proteins are found in all three domains of life as inte ...
- DOI:
- 10.1111/1462-2920.14071
-
http://dx.doi.org/10.1111/1462-2920.14071
- Author:
- Gong, Weida; Paerl, Hans; Marchetti, Adrian
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1095-1111
- ISSN:
- 1462-2912
- Subject:
- biochemical pathways; carbon metabolism; environmental factors; estuaries; eutrophication; gene expression; genes; nitrogen; phytoplankton; polysaccharides; rivers; water quality
- Abstract:
- ... Over the span of a year, we investigated the interactions between biotic and abiotic factors within the eutrophic Neuse River Estuary (NRE). Through metatranscriptomic sequencing in combination with water quality measurements, we show that there are different metabolic strategies deployed along the NRE. In the upper estuary, taxonomically resolved phytoplankton groups express more transcripts of g ...
- DOI:
- 10.1111/1462-2920.14049
-
http://dx.doi.org/10.1111/1462-2920.14049
- Author:
- Shen, Dandan; Jürgens, Klaus; Beier, Sara
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1170-1184
- ISSN:
- 1462-2912
- Subject:
- bacteria; bacterioplankton; environmental factors; habitats; phylogeny; salinity; Baltic Sea
- Abstract:
- ... The response of local communities to marine–freshwater transitions and the processes that underlie community assembly are unclear, particularly with respect to bacteria that differ in their life strategies. Here, we implemented a transplant experiment where bacterioplankton from three regions of the Baltic Sea with differing salinities (∼3, 7 and 28 psu) were exposed to each other's environmental ...
- DOI:
- 10.1111/1462-2920.14059
-
http://dx.doi.org/10.1111/1462-2920.14059
- Author:
- Topçuoğlu, Begüm D.; Meydan, Cem; Orellana, Roberto; Holden, James F.
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 949-957
- ISSN:
- 1462-2912
- Subject:
- Thermococcus; formate dehydrogenase; formates; gene expression regulation; heterotrophs; hydrogen; hydrogen production; maltose; operon; oxidation; secretion; sequence analysis; tryptones
- Abstract:
- ... Some hyperthermophilic heterotrophs in the genus Thermococcus produce H₂ in the absence of S° and have up to seven hydrogenases, but their combined physiological roles are unclear. Here, we show which hydrogenases in Thermococcus paralvinellae are affected by added H₂ during growth without S°. Growth rates and steady‐state cell concentrations decreased while formate production rates increased when ...
- DOI:
- 10.1111/1462-2920.14022
- Chorus Open Access:
- 10.1111/1462-2920.14022
-
http://dx.doi.org/10.1111/1462-2920.14022
- Author:
- Eichorst, Stephanie A.; Trojan, Daniela; Roux, Simon; Herbold, Craig; Rattei, Thomas; Woebken, Dagmar
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1041-1063
- ISSN:
- 1462-2912
- Subject:
- Acidobacteria; bacteriophages; carbohydrates; ecophysiology; edaphic factors; genome; genomics; hydrogen; nitrogen; oxygen; peptidases; sequence analysis; soil; soil bacteria
- Abstract:
- ... Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large‐scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile element ...
- DOI:
- 10.1111/1462-2920.14043
- PubMed:
- 29327410
- PubMed Central:
- PMC5900883
-
http://dx.doi.org/10.1111/1462-2920.14043
- Author:
- Heger, Thierry J.; Giesbrecht, Ian J. W.; Gustavsen, Julia; del Campo, Javier; Kellogg, Colleen T. E.; Hoffman, Kira M.; Lertzman, Ken; Mohn, William W.; Keeling, Patrick J.
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1185-1203
- ISSN:
- 1462-2912
- Subject:
- Filasterea; bogs; calcium; community structure; drainage; edaphic factors; forest ecosystems; forest trees; fungi; habitats; high-throughput nucleotide sequencing; landscapes; mosses and liverworts; phylogeny; primary productivity; protists; rain forests; soil; species diversity; British Columbia
- Abstract:
- ... Although previous studies, mostly based on microscopy analyses of a few groups of protists, have suggested that protists are abundant and diverse in litter and moss habitats, the overall diversity of moss and litter associated protists remains elusive. Here, high‐throughput environmental sequencing was used to characterize the diversity and community structure of litter‐ and moss‐associated protis ...
- DOI:
- 10.1111/1462-2920.14061
-
http://dx.doi.org/10.1111/1462-2920.14061
- Author:
- Rummens, Koen; De Meester, Luc; Souffreau, Caroline
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1120-1133
- ISSN:
- 1462-2912
- Subject:
- aquatic bacteria; bacterial communities; bacterioplankton; community structure; freshwater; genotype; inoculum; ponds; population structure
- Abstract:
- ... Priority effects occur when the arrival order of species or genotypes has a lasting effect on community or population structure. For freshwater bacteria, priority effects have been shown experimentally among individual species, but no experiments have been performed using complex natural communities. We investigated experimentally whether a foreign bacterioplankton community influences the communi ...
- DOI:
- 10.1111/1462-2920.14053
-
http://dx.doi.org/10.1111/1462-2920.14053
- Author:
- Lv, Haoxin; Sahin, Nurettin; Tani, Akio
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1204-1223
- ISSN:
- 1462-2912
- Subject:
- Burkholderia ambifaria; Cupriavidus necator; Dyadobacter; Gram-negative bacteria; Methylophilus; genes; genomics; methanol; methylamine; nucleotide sequences; quantitative polymerase chain reaction; rhizosphere; ribosomal RNA; ribulose; rice; soil; transfer RNA
- Abstract:
- ... Recently, it has been found that two types of methanol dehydrogenases (MDHs) exist in Gram‐negative bacterial methylotrophs, calcium‐dependent MxaFI‐MDH and lanthanide‐dependent XoxF‐MDH and the latter is more widespread in bacterial genomes. We aimed to isolate and characterize lanthanide‐dependent methylotrophs. The growth of strain La2‐4ᵀ on methanol, which was isolated from rice rhizosphere so ...
- DOI:
- 10.1111/1462-2920.14062
-
http://dx.doi.org/10.1111/1462-2920.14062
- Author:
- Maciá‐Vicente, Jose G.; Shi, Yan‐Ni; Cheikh‐Ali, Zakaria; Grün, Peter; Glynou, Kyriaki; Kia, Sevda Haghi; Piepenbring, Meike; Bode, Helge B.
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1253-1270
- ISSN:
- 1462-2912
- Subject:
- chemotaxonomy; endophytes; fungi; phylogeny
- Abstract:
- ... Fungi are prolific producers of natural products routinely screened for biotechnological applications, and those living endophytically within plants attract particular attention because of their purported chemical diversity. However, the harnessing of their biosynthetic potential is hampered by a large and often cryptic phylogenetic and ecological diversity, coupled with a lack of large‐scale natu ...
- DOI:
- 10.1111/1462-2920.14072
-
http://dx.doi.org/10.1111/1462-2920.14072
- Author:
- Ji, Nanjing; Lin, Lingxiao; Li, Ling; Yu, Liying; Zhang, Yaqun; Luo, Hao; Li, Meizhen; Shi, Xinguo; Wang, Da‐Zhi; Lin, Senjie
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1078-1094
- ISSN:
- 1462-2912
- Subject:
- Raphidophyceae; algae; algal blooms; carbon dioxide fixation; carbonate dehydratase; genes; phosphates; phosphorus; photosynthesis; phytoplankton; ribosomal DNA; East China Sea
- Abstract:
- ... Despite numerous laboratory studies on physiologies of harmful algal bloom (HAB) species, physiologies of these algae during a natural bloom are understudied. Here, we investigated a bloom of the raphidophyte Heterosigma akashiwo in the East China Sea in 2014 using metabarcode (18S rDNA) and metatranscriptome sequencing. Based on 18S rDNA analyses, the phytoplankton community shifted from high div ...
- DOI:
- 10.1111/1462-2920.14045
-
http://dx.doi.org/10.1111/1462-2920.14045
- Author:
- Chen, Shuaimin; Wang, Fenghua; Zhang, Yuming; Qin, Shuping; Wei, Shoucai; Wang, Shiqin; Hu, Chunsheng; Liu, Binbin
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 980-992
- ISSN:
- 1462-2912
- Subject:
- Pseudomonas; denitrification; denitrifying microorganisms; genes; leaching; nitrates; nitrogen; nitrous oxide; organic carbon; soil profiles; vadose zone
- Abstract:
- ... Microbes in the deep vadose zone play an essential role in the mitigation of nitrate leaching; however, limited information is available on the mechanisms of microbial denitrification due to sampling difficulties. We experimentally studied the factors that affect denitrification in soils collected down to 10.5 meters deep along the soil profile. After an anoxic pre‐incubation, denitrification rate ...
- DOI:
- 10.1111/1462-2920.14027
-
http://dx.doi.org/10.1111/1462-2920.14027
- Author:
- Atashgahi, Siavash; Häggblom, Max M.; Smidt, Hauke
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 934-948
- ISSN:
- 1462-2912
- Subject:
- anthropogenic activities; bacteria; biodegradation; energy; evolution; halogens; organic halogen compounds; tundra; tundra soils
- Abstract:
- ... Halogenated organic compounds, also termed organohalogens, were initially considered to be of almost exclusively anthropogenic origin. However, over 5000 naturally synthesized organohalogens are known today. This has also fuelled the hypothesis that the natural and ancient origin of organohalogens could have primed development of metabolic machineries for their degradation, especially in microorga ...
- DOI:
- 10.1111/1462-2920.14016
- Chorus Open Access:
- 10.1111/1462-2920.14016
-
http://dx.doi.org/10.1111/1462-2920.14016
- Author:
- Zhang, Xing; St. Leger, Raymond J.; Fang, Weiguo
- Source:
- Environmental microbiology 2018 v.20 no.3 pp. 1158-1169
- ISSN:
- 1462-2912
- Subject:
- Metarhizium robertsii; cross immunity; fermentation; fungi; genes; heat stress; microbial growth; oxidative stress; pyruvic acid; quantitative polymerase chain reaction; reactive oxygen species; reverse transcriptase polymerase chain reaction; salt stress; sequence analysis; trichloroacetic acid
- Abstract:
- ... It is commonly observed that microorganisms subjected to a mild stress develop tolerance not only to higher doses of the same stress but also to other stresses – a phenomenon called cross protection. The mechanisms for cross protection have not been fully revealed. Here, we report that heat shock induced cross protection against UV, oxidative and osmotic/salt stress conditions in the cosmopolitan ...
- DOI:
- 10.1111/1462-2920.14058
-
http://dx.doi.org/10.1111/1462-2920.14058