Showing papers in "FEMS Microbiology Ecology in 2016"

TL;DR: The present review describes the most recent advances in understanding the ecological functions of Trichodermaspp.

TL;DR: It is argued that practices used in plant breeding, seed treatments and agriculture are among the reasons for the loss of fungal endophytes diversity in domesticated plants and accounts for the reduced effectiveness of some endophyte strains to confer plant benefits.

TL;DR: A unique experimental design coupled to high-throughput sequencing of ribosomal markers is applied to characterize the microbiota at the long-term alpine permafrost study site 'Muot-da-Barba-Peider' in eastern Switzerland with an approximate radiocarbon age of 12 000 years, yielding an unprecedented view on microbial life in temperate mountain permaf frost.

TL;DR: The advantages of the majority of this versatile and diverse group of microorganisms for plant health and growth as demonstrated by their contribution to disease-suppressive soils, their antifungal and antibacterial activities, their ability to produce volatile compounds and their capacity to enhance plant biomass are discussed.

TL;DR: The high ammonia tolerance of ‘Ca. N. franklandus’ suggests potential contributions to nitrification in fertilised soils and reduces support for niche differentiation between soil AOA and AOB and suggests that AOA have a wider physiological diversity than previously suspected.

TL;DR: This review focuses on methods used for biopriming, and also the role in improving crop productivity and stress tolerance along with prospects of this technology.

TL;DR: Wastewater discharge enriched only a few genes, namely Tn25 type transposase gene and clinical class 1 integrons, in the sediment near the discharge pipe, but those enriched genes may indicate a potential for horizontal gene transfer.

TL;DR: This minireview considers what is currently known about bacteria in wood and their interactions with fungi, and proposes possible associations based on examples from other habitats, to identify key knowledge gaps and pressing questions for future research.

TL;DR: This review highlights selected case studies of endophytes and discusses their lifestyles and behavioural traits, and discusses how these factors contribute towards their effectiveness as biological control agents.

TL;DR: Results indicate that Saccharibacteria is a phylogenetically diverse group and play a role in the degradation of various organic compounds as well as sugar compounds under aerobic-, nitrate reducing- and anaerobic conditions.

TL;DR: The fish farm resistomes were enriched in transposon and integron associated genes and in ARGs encoding resistance to antibiotics which had been used to treat fish at the farms, suggesting that there is a natural Baltic sediment resistome.

TL;DR: Results showed that plant epiphytic communities either decreased to low relative abundances or disappeared following rumen incubation, and that temporal colonization of the PRG by the rumen bacteria was biphasic with primary and secondary events evident with the transition period being with 2-4 h.

TL;DR: The results demonstrate that in a medium-term study the combination of qPCR and next generation sequencing corroborated by drug-related health data is a suitable approach to characterize seasonal changes of ARGs in wastewater and treated wastewater.

TL;DR: Analysis of 16S rRNA gene transcript amplicon sequencing in a temperate grassland soil subjected to century-long exposure to normal or extremely high copper levels showed that bioavailable copper had pronounced impacts on the structure of the transcriptionally active bacterial community, overruling other environmental factors.

TL;DR: The human and mammalian gut microbiomes contain the widest diversity of clinically relevant resistance genes using metagenomic analysis, and the human microbiomes contained a high relative abundance of resistance genes, while the relative abundances varied greatly in the marine and soil metagenomes.

TL;DR: The ability of ITALIC!

TL;DR: It is shown that both neutral and niche processes played a critical role in the assembly of entire bacterial communities, shaping a unique biogeographical pattern in 21 plateau lakes of China.

TL;DR: Initial evidence for a recent interspecies transmission of a new successful clone of ST410 E. coli between wildlife, humans, companion animals and the environment is given to underline the zoonotic potential of clinically relevant multi-resistant bacteria found in the environment as well as the mandatory nature of the 'One Health' approach.

TL;DR: Data synthesized show that the shale microbial community predictably shifts in response to temporal changes in geochemistry, favoring conservation of key microorganisms regardless of inputs, shale location or operators.

TL;DR: The bacterial community dynamics reflects changes in the availability of possible resources either of the plant or microbial origin, especially later in the decomposition process when its abundance increases.

TL;DR: This study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs.

TL;DR: The wide distribution of Methanomassiliicoccales in wetlands is highlighted, which suggests that they contribute to methane emissions from these climate-relevant ecosystems.

TL;DR: The importance of B. bifidum as a microbial biomarker for UC is highlighted by revealing its role in protection against experimentally induced colitis, as shown by the increase in the expression of many tight junction-encoding genes.

TL;DR: This work used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea, detecting a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences.

TL;DR: This study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone, which is suitable for distinguishing species in the majority of lineages in the genus.

TL;DR: Overall, forest topsoil should be considered a spatially heterogeneous environment in which the mean estimates of ecosystem-level processes and microbial community composition may confound the existence of highly specific microenvironments.

TL;DR: The ability of metal-resistant DSE strains to produce both soluble and volatile compounds for plant growth promotion indicates interesting microbial resources with high potential to support sustainable production of bioenergy crops within the context of the phytomanagement ofMetal-contaminated sites.

TL;DR: It is demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated, and CLPP revealed site-specific effects.

TL;DR: The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.

TL;DR: Slurry incubations of Italian paddy field soil with nitrate and 13C-labelled methane have the potential for nitrate-dependent anaerobic oxidation of methane (79.9 nmol g-1dw d-1) and data suggest an important role of AAA in methane cycling in paddy fields.