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Environmental Microbiology Reports

Lucie A Malard, David A Pearce
Microorganisms dominate terrestrial environments in the polar regions and Arctic soils are known to harbour significant microbial diversity, far more diverse and numerous in the region than was once thought. Furthermore, the geographic distribution and structure of Arctic microbial communities remains elusive, despite their important roles in both biogeochemical cycling and in the generation and decomposition of climate active gases. Critically, Arctic soils are estimated to store over 1500 Pg of carbon and thus, have the potential to generate positive feedback within the climate system...
July 20, 2018: Environmental Microbiology Reports
Katherine R Heal, Wei Qin, Shady A Amin, Allan H Devol, James W Moffett, E Virginia Armbrust, David A Stahl, Anitra E Ingalls
Cobalamin (vitamin B12 ) is a precious resource in natural systems that is produced by select prokaryotes and required by a broad range of organisms. In this way, the production of cobalamin reinforces numerous microbial interdependencies. Here we report the accumulation of an unusual form of cobalamin, nitrocobalamin (NO2 -cobalamin), in a marine oxygen deficient zone (ODZ), isolates of ammonia-oxidizing archaea (AOA), and an anaerobic ammonium oxidizing bacteria (anammox) enriched bioreactor. Low oxygen waters were enriched in NO2 -cobalamin, and AOA isolates experiencing ammonia or copper stress produced more NO2 -cobalamin, though there is wide strain-to-strain and batch-to-batch variability...
July 18, 2018: Environmental Microbiology Reports
Andrea Di Cesare, Sara Petrin, Diego Fontaneto, Carmen Losasso, Ester M Eckert, Giovanni Tassistro, Alessio Borello, Antonia Ricci, William H Wilson, Carla Pruzzo, Luigi Vezzulli
Antibiotic resistance is a rising threat for human health. Although in clinical settings and terrestrial environments the rise of antibiotic resistant bacteria is well documented, their dissemination and spread in the marine environment, covering almost two-thirds of the Earth's surface, is still poorly understood. In this study, the presence and abundance of sulphonamide resistance gene (sul2) and class 1 integron-integrase gene (intI1), used as markers for the occurrence and spread of antibiotic resistance genes since the beginning of the antibiotic era, were investigated...
July 18, 2018: Environmental Microbiology Reports
Cuixiao Xie, Kaikai Sun, Kai Zhang, Yongge Sun, Zhenmei Lu
Cyanobacteria are important primary producers on the surface of oceans and are susceptible to oil spills. However, their tolerance to oil and their roles in the bioremediation of crude oil remain elusive. We analyzed the response of microbial communities to a simulated oil spill in estuarine sediment microcosms under a series of oil concentrations (0, 25, 125 and 250 g kg-1 .dry wt.). Cyanobacterial blooms only occurred on the sediment surface in the low oil (LO, 25 g kg-1 .dry wt.) group, and cyanobacteria grew from very small amounts to enriched levels according to an internal mechanism...
July 18, 2018: Environmental Microbiology Reports
Konstantin von Gunten, Stewart M Hamilton, Cheng Zhong, Camilla Nesbø, Jiaying Li, Karlis Muehlenbachs, Kurt O Konhauser, Daniel S Alessi
Forest rings are 50-1600 m diameter circular structures found in boreal forests around the globe. They are believed to be chemically reducing chimney features, having an accumulation of reduced species in the middle of the ring and oxidation processes occurring at the ring's edges. It has been suggested that microorganisms could be responsible for charge transfer from the inside to the outside of the ring. To explore this, we focused on the changes in bacterial and archaeal communities in the ring edges of two forest rings, the "Bean" and the "Thorn North" ring, in proximity to each other in Ontario, Canada...
July 16, 2018: Environmental Microbiology Reports
Takashi Hayakawa, Senthilvel K S S Nathan, Danica J Stark, Diana A Ramirez Saldivar, Rosa Sipangkui, Benoit Goossens, Augustine Tuuga, Marcus Clauss, Akiko Sawada, Shinji Fukuda, Hiroo Imai, Ikki Matsuda
Foregut fermentation is well known to occur in a wide range of mammalian species and in a single bird species. Yet, the foregut microbial community of free-ranging, foregut-fermenting monkeys, i.e., colobines, has not been investigated so far. We analyzed the foregut microbiomes in four free-ranging proboscis monkeys (Nasalis larvatus) from two different tropical habitats with varying plant diversity (mangrove and riverine forests), in an individual from a semi-free-ranging setting with supplemental feeding, and in an individual from captivity, using high-throughput sequencing based on 16S ribosomal RNA genes...
July 11, 2018: Environmental Microbiology Reports
Djuna Gulliver, Daniel Lipus, Daniel Ross, Kyle Bibby
Geological carbon storage is likely to be part of a comprehensive strategy to minimize the atmospheric release of carbon dioxide (CO2 ), raising concerns that injected CO2 will leak into overlying freshwater aquifers. CO2(aq) leakage may impact the dominant microbial community responsible for important ecosystem functions such as nutrient cycling, metal cycling, and carbon conversion. Here, we examined the impact of in situ CO2 leakage on a freshwater aquifer microbial community. High-throughput 16S rRNA gene sequencing demonstrated lower microbial diversity in freshwater wells with CO2 concentrations above 1...
July 8, 2018: Environmental Microbiology Reports
Kana Morinaga, Tatsuya Yamamoto, Nobuhiko Nomura, Masanori Toyofuku
Many Gram-negative bacteria utilize N-acyl homoserine lactone (AHL) signals to communicate with each other. Once they have been released, these signals are assumed to be shared among the population in the local environment. In contrast to this canonical quorum-sensing (QS) model, recent study in Paracoccus denitrificans showed that they can traffic their signals to each other via membrane vesicles (MVs). Here, we demonstrate that various long-chain AHLs inhibited cell aggregation in P. denitrificans, while the short-chain AHLs alone did not...
July 2, 2018: Environmental Microbiology Reports
Jie-Ling Lai, Dong-Jie Tang, Yu-Wei Liang, Ren Zhang, Qi Chen, Zhen-Ping Qin, Zhen-Hua Ming, Ji-Liang Tang
The RNA chaperone, Hfq, is known to play extensive roles in bacterial growth and development. More recently, it has been shown to be required for virulence in many human and animal bacterial pathogens. Despite these studies little is known about the role Hfq plays in phytopathogenic bacteria. In this study, we show Hfq is required for full virulence of the crucifer black rot pathogen Xanthomonas campestris pv. campestris (Xcc). We demonstrate that an Xcc hfq deletion strain is highly attenuated for virulence in Chinese radish and shows a severe defect in the production of virulence factors including extracellular enzymes and extracellular polysaccharide...
June 14, 2018: Environmental Microbiology Reports
Gregg S Pettis
The hallmark of mycelial spore-forming bacteria of the genus Streptomyces is their prolific production of antibiotics and other bioactive secondary metabolites as part of a complex morphological and physiological developmental program. They are further distinguished by a conjugation mechanism that differs substantially from the single-strand mode of DNA transfer via Type IV secretion, which is exhibited by numerous unicellular Gram-negative and Gram-positive bacteria. At the crux of the novel intermycelial transfer event in Streptomyces spp...
June 14, 2018: Environmental Microbiology Reports
Hiroyuki Iguchi, Yusuke Yoshida, Kento Fujisawa, Hiroki Taga, Hiroya Yurimoto, Tokitaka Oyama, Yasuyoshi Sakai
KaiC protein is the pivotal component of the circadian clock in cyanobacteria. While KaiC family proteins are well conserved throughout divergent phylogenetic lineages, studies of the physiological roles of KaiC proteins from other microorganisms have been limited. We examined the role of the KaiC proteins, KaiC1 and KaiC2, in the methanol-utilizing bacterium Methylobacterium extorquens AM1. Wild-type M. extorquens AM1 cells exhibited temperature-dependent UV resistance (TDR) under permissive growth temperatures (24-32°C)...
June 14, 2018: Environmental Microbiology Reports
Ram P Maharjan, Thomas Ferenci
Genetic variation in bacterial populations is remarkably sensitive to environmental influences, including simple, nutritional differences. Not only the rate but also the kind of mutational changes is biased by the nutritional state of bacteria. Here we investigate the mutational consequences of a universal variable for free-living bacteria, namely the growth rate. By controlling growth in chemostats, the rate and mix of mutations was investigated for populations of Escherichia coli subject to different specific growth rates...
May 24, 2018: 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
Lawrence P Wackett
No abstract text is available yet for this article.
June 2018: Environmental Microbiology Reports
Martin Grafe, Manuela Goers, Sabine von Tucher, Christel Baum, Dana Zimmer, Peter Leinweber, Gisle Vestergaard, Susanne Kublik, Michael Schloter, Stefanie Schulz
Phosphorus is one of the most important macronutrient 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...
June 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...
June 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...
June 2018: Environmental Microbiology Reports
Burdukiewicz Michał, Przemysław Gagat, Sławomir Jabłoński, Jarosław Chilimoniuk, Michał Gaworski, Paweł Mackiewicz, Łukaszewicz Marcin
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 is 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...
June 2018: Environmental Microbiology Reports
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