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Environmental Microbiology Reports

Johanna Sjöstedt, Silke Langenheder, Emma Kritzberg, Christofer M G Karlsson, Eva S Lindström
Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance...
May 7, 2018: Environmental Microbiology Reports
Andriy Kovalchuk, Mukrimin Mukrimin, Zhen Zeng, Tommaso Raffaello, Mengxia Liu, Risto Kasanen, Hui Sun, Fred O Asiegbu
Plant microbiome plays an important role in maintaining the host fitness. Despite a significant progress in our understanding of the plant microbiome achieved in the recent years, very little is known about the effect of plant pathogens on composition of microbial communities associated with trees. In this study, we analyzed the mycobiome of different anatomic parts of asymptomatic and symptomatic Norway spruce trees naturally infected by Heterobasidion spp. We also investigated the primary impact of the disease on the fungal communities, which are associated with Norway spruce trees...
May 4, 2018: Environmental Microbiology Reports
Cristina Díez-Vives, Ana I S Esteves, Rodrigo Costa, Shaun Nielsen, Torsten Thomas
Sponges interact with diverse and rich communities of bacteria that are phylogenetically often distinct from their free-living counterparts. Recent genomics and metagenomic studies have indicated that bacterial sponge symbionts also have distinct functional features from free-living bacteria, however it is unclear, if such genome-derived functional signatures are common and present in different symbiont taxa. We therefore compared here a large set of genomes from cultured (Pseudovibrio, Ruegeria, Aquimarina) and yet-uncultivated (Synechococcus) bacteria found either in sponge-associated or free-living sources...
April 30, 2018: Environmental Microbiology Reports
Martin Grafe, Manuela Goers, Sabine V Tucher, Christel Baum, Dana Zimmer, Peter Leinweber, Gisle Vestergaard, Susanne Kublik, Michael Schloter, Stefanie Schulz
Phosphorous is one of the most important macronutrients for plants. In agriculture, amending fertilizer with phosphorus (P) is common practice. However, natural phosphorus sources are finite, making research for more sustainable management practices necessary. We postulated that the addition of carbon (C) and nitrogen (N) would stimulate phosphorus mobilization by bacteria because of their desire to maintain a stable intracellular C:N:P stoichiometry. Therefore, we chose a metagenomic approach to investigate two agricultural soils, which only received mineral N fertilizer or mineral N and organic fertilizer for more than 20 years...
April 24, 2018: Environmental Microbiology Reports
Sheo Shankar Pandey, Pradeep Kumar Patnana, Yasobanta Padhi, Subhadeep Chatterjee
Expression of hrp (hypersensitive reaction and pathogenicity) genes inside the host is crucial for virulence of phytopathogenic bacteria. The hrp genes encode components of type3 secretion system (T3SS), HR elicitors and several regulators, which are involved in the co-ordinated expression of hrp genes in the host environment and in hrp inducing chemically defined medium. However, little is known about specific host or environmental factors which may play a role in the induction of hrp gene expression. In this study, we show that iron-limiting condition elicits induced expression of hrp genes, including type3 secretion system (T3SS) and effectors (T3E)...
April 24, 2018: Environmental Microbiology Reports
Jia Liu, Wenyan Zhang, Haijian Du, Xiaoyun Leng, Jin-Hua Li, Hongmiao Pan, Jianhong Xu, Long-Fei Wu, Tian Xiao
There are two genetically distinct morphological types of multicellular magnetotactic prokaryotes (MMPs) in the intertidal zone of Lake Yuehu (China): ellipsoidal MMPs (eMMPs) and spherical MMPs (sMMPs). We studied the vertical distribution of both types of MMPs in the sediment at Lake Yuehu during one year. Both types of MMPs were observed at sediment depths ranging from 1 to 34 cm, depending on the seasons. The eMMPs distributed at depths of 2-34 cm during spring, 1-11 cm during summer, 2-21 cm during autumn, and 9-32 cm during winter...
April 24, 2018: Environmental Microbiology Reports
Victoria Rutherford, Kelly Yom, Egon A Ozer, Olivia Pura, Ami Hughes, Katherine R Murphy, Laura Cudzilo, David Mitchel, Alan R Hauser
Pseudomonas aeruginosa uses its type III secretion system to inject the effector proteins ExoS and ExoU into eukaryotic cells, which subverts these cells to the bacterium's advantage and contributes to severe infections. We studied the environmental reservoirs of exoS+ and exoU+ strains of P. aeruginosa by collecting water, soil, moist substrates, and plant samples from environments in the Chicago region and neighboring states. Whole-genome sequencing was used to determine the phylogeny and type III secretion system genotypes of 120 environmental isolates...
April 24, 2018: Environmental Microbiology Reports
Magdalena Kopycińska, Paulina Lipa, Jolanta Cieśla, Marta Kozieł, Monika Janczarek
Rhizobium leguminosarum bv. trifolii is a soil bacterium that establishes symbiosis with clover (Trifolium spp.) under nitrogen-limited conditions. This microorganism produces exopolysaccharide (EPS), which plays an important role in symbiotic interactions with the host plant. The aim of the current study was to establish the role of EPS in the response of R. leguminosarum bv. trifolii cells, free-living and during symbiosis, to zinc stress. We show that EPS-deficient mutants were more sensitive to Zn2+ exposure than EPS-producing strains, and that EPS overexpression conferred some protection onto the strains beyond that observed in the wild type...
April 6, 2018: Environmental Microbiology Reports
Alexandra A Popova, Ulla Rasmussen, Tatiana A Semashko, Vadim M Govorun, Olga A Koksharova
Various species of cyanobacteria, diatoms and dinoflagellates are capable of synthesizing the non-proteinogenic neurotoxic amino acid β-N-methylamino-L-alanine (BMAA), which is known to be a causative agent of human neurodegeneration. Similar to most cyanotoxins, the biological and ecological functions of BMAA in cyanobacteria are unknown. In this study, we show for the first time that BMAA, in micromolar amounts, inhibits the formation of heterocysts (specialized nitrogen-fixing cells) in heterocystous, diazotrophic cyanobacteria (Anabaena sp...
April 6, 2018: Environmental Microbiology Reports
Eva C Sonnenschein, Christopher Broughton William Phippen, Mikkel Bentzon-Tilia, Silas Anselm Rasmussen, Kristian Fog Nielsen, Lone Gram
The Roseobacter-group species Phaeobacter inhibens produces the antibacterial tropodithietic acid (TDA) and the algaecidal roseobacticides with both compound classes sharing part of the same biosynthetic pathway. The purpose of this study was to investigate the production of roseobacticides more broadly in TDA-producing roseobacters and to compare the effect of producers and non-producers on microalgae. Of 33 roseobacters analyzed, roseobacticide production was a unique feature of TDA-producing P. inhibens, P...
April 6, 2018: Environmental Microbiology Reports
Michał Burdukiewicz, Przemysław Gagat, Sławomir Jabłoński, Jarosław Chilimoniuk, Michał Gaworski, Paweł Mackiewicz, Marcin Łukaszewicz
The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotechnological purposes. An important component of the understudied ecosystems are methanogens, archaea producing a potent greenhouse-effect gas methane. Therefore, we created PhyMet2 , the first database that combines descriptions of methanogens and their culturing conditions with genetic information...
April 6, 2018: Environmental Microbiology Reports
Torahiko Okubo, Mizue Matsushita, Shinji Nakamura, Junji Matsuo, Hiroki Nagai, Hiroyuki Yamaguchi
Soil-borne amoeba Acanthamoeba S13WT has an endosymbiotic relationship with an environmental Neochlamydia bacterial strain. However, regardless of extensive experiments in liquid media, the biological advantage of the symbiosis remained elusive. We therefore explored the role of the endosymbiont in predator-prey interactions on solid media. A mixed culture of the symbiotic or aposymbiotic amoebae and GFP-expressing Escherichia coli or Salmonella Enteritidis was spotted onto the center of a LB or B-CYE agar plate pre-inoculated with a ring of mCherry-expressing Legionella pneumophila (Legionella "wall")...
April 3, 2018: Environmental Microbiology Reports
D Rodelli, L Jovane, A P Roberts, J Cypriano, F Abreu, U Lins
Magnetotactic bacteria are a multi-phyletic group of bacteria that synthesize membrane-bound magnetic minerals. Understanding the preservation of these minerals in various environments (e.g. with varying oxygen concentrations and iron supply) is important for understanding their role as carriers of primary magnetizations in sediments and sedimentary rocks. Here we present X-ray near edge structure (XANES) spectra for Fe in magnetotactic bacteria samples from recent sediments to assess surface oxidation and crystal structure changes in bacterial magnetite during early burial...
April 3, 2018: Environmental Microbiology Reports
Bryony A P Williams, Kristina M Hamilton, Meredith D Jones, David Bass
The description of diversity is a key imperative in current biological studies and has been revolutionised by the molecular era that allows easy access to microbial diversity not visible to the naked eye. Broadly-targeted SSU rRNA gene amplicon studies of diverse environmental habitats continue to reveal new microbial eukaryotic diversity. However, some eukaryotic lineages, particularly parasites, have divergent SSU sequences, and are therefore undersampled or excluded by the methodologies used for SSU studies...
March 26, 2018: Environmental Microbiology Reports
Yang Zhou, Honghui Zhu, Qing Yao
Phosphorus (P) cycling is a fundamental process driven by microorganisms, and plants can regulate P cycling directly or via their influence on the soil microbial community. However, the differential P cycling patterns associated with legumes and grass are largely unknown. Therefore, we investigated the microbial community involved in P cycling in subtropical soil grown with stylo (Stylosanthes guianensis, legume) or bahiagrass (Paspalum notatum, grass) using metagenomic sequencing. P fractionation indicated that sparingly soluble inorganic P (Pi) accounted for approximately 75% of P pool...
March 24, 2018: Environmental Microbiology Reports
Carolina N Keim, Roger Duarte de Melo, Fernando P Almeida, Henrique G P Lins de Barros, Marcos Farina, Daniel Acosta-Avalos
Magnetotactic bacteria are found in the chemocline of aquatic environments worldwide. They produce nanoparticles of magnetic minerals arranged in chains in the cytoplasm, which enable these microorganisms to align to magnetic fields while swimming propelled by flagella. Magnetotactic bacteria are diverse phylogenetically and morphologically, including cocci, rods, vibria, spirilla and also multicellular forms, known as Magnetotactic Multicellular Prokaryotes (MMPs). We used video-microscopy to study the motility of the uncultured MMP 'Candidatus Magnetoglobus multicellularis' under applied magnetic fields ranging from 0...
March 24, 2018: Environmental Microbiology Reports
Delyana Vasileva, Chiho Suzuki-Minakuchi, Saori Kosono, Minoru Yoshida, Kazunori Okada, Hideaki Nojiri
Understanding the interplay between a plasmid and its host system is a bottleneck towards prediction of the fate of plasmid-harbouring strains in the natural environments. Here, we studied the impact of the conjugative plasmid pCAR1, involved in carbazole degradation, on the proteome of Pseudomonas putida KT2440 by using SILAC method. Furthermore, we investigated two acyl lysine modifications (acetylation and succinylation) that respond to the metabolic status of the cell and are implicated in regulation of various cellular processes...
March 24, 2018: Environmental Microbiology Reports
Jasmin Frey, Fabian Schneider, Thomas Huhn, Dieter Spiteller, Bernhard Schink, David Schleheck
Degradation of acetone by the sulfate-reducing bacterium Desulfococcus biacutus involves an acetone-activation reaction different from that used by aerobic or nitrate-reducing bacteria, because the small energy budget of sulfate-reducing bacteria does not allow for major expenditures into ATP-consuming carboxylation reactions. In the present study, an inducible coenzyme B12 -dependent conversion of 2-hydroxyisobutyryl-CoA to 3-hydroxybutyryl-CoA was demonstrated in cell-free extracts of acetone-grown D. biacutus cells, together with a NAD+ -dependent oxidation of 3-hydroxybutyryl-CoA to acetoacetyl-CoA...
March 12, 2018: Environmental Microbiology Reports
Jianqiang Miao, Xiuhuan Li, Dong Lin, Xili Liu, Brett M Tyler
Oxysterol-binding protein (OSBP)-related proteins (ORPs) are a large conserved family of lipid transfer proteins in eukaryotes. In oomycetes, some ORPs are the target of the novel oomycide oxathiapiprolin. By searching the Phytophthora sojae genome database, two ORP proteins, PsORP1 (Protein ID: 558498) and PsORP2 (Protein ID: 470921), were found. Here, we investigated the biological function of PsORP2. The expression level of PsORP2 was higher in germinated cysts and late infection than in other developmental stages...
March 9, 2018: Environmental Microbiology Reports
Jesse M Wilson, Steven Y Litvin, J Michael Beman
Respiration of organic material is a central process in the global carbon (C) cycle catalysed by diverse microbial communities. In the coastal ocean, upwelling can drive variation in both community respiration (CR) and the microbial community, but linkages between the two are not well-understood. We measured CR rates and analysed microbial dynamics via 16S rRNA gene sequencing, to assess whether CR correlated with upwelling irrespective of changes in the microbial community, or if the particular microbial community present was a factor in explaining variations in CR...
February 28, 2018: Environmental Microbiology Reports
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