Bacteria and fungi respond differently to multifactorial climate change in a temperate heathland, traced with ¹³C-Glycine and FACE CO₂

It is vital to understand responses of soil microorganisms to predicted climate changes, as these directly control soil carbon (C) dynamics. The rate of turnover of soil organic carbon is mediated by soil microorganisms whose activity may be affected by climate change. After one year of multifactorial climate change treatments, at an undisturbed temperate heathland, soil microbial community dynamics were investigated by injection of a very small concentration (5.12 µg C g(-1) soil) of (13)C-labeled glycine ((13)C2, 99 atom %) to soils in situ. Plots were treated with elevated temperature (+1°C, T), summer drought (D) and elevated atmospheric carbon dioxide (510 ppm [CO2]), as well as combined treatments (TD, TCO2, DCO2 and TDCO2). The (13)C enrichment of respired CO2 and of phospholipid fatty acids (PLFAs) was determined after 24 h. (13)C-glycine incorporation into the biomarker PLFAs for specific microbial groups (Gram positive bacteria, Gram negative bacteria, actinobacteria and fungi) was quantified using gas chromatography-combustion-stable isotope ratio mass spectrometry (GC-C-IRMS). Gram positive bacteria opportunistically utilized the freshly added glycine substrate, i.e. incorporated (13)C in all treatments, whereas fungi had minor or no glycine derived (13)C-enrichment, hence slowly reacting to a new substrate. The effects of elevated CO2 did suggest increased direct incorporation of glycine in microbial biomass, in particular in G(+) bacteria, in an ecosystem subjected to elevated CO2. Warming decreased the concentration of PLFAs in general. The FACE CO2 was (13)C-depleted (δ(13)C = 12.2‰) compared to ambient (δ(13)C = ∼-8‰), and this enabled observation of the integrated longer term responses of soil microorganisms to the FACE over one year. All together, the bacterial (and not fungal) utilization of glycine indicates substrate preference and resource partitioning in the microbial community, and therefore suggests a diversified response pattern to future changes in substrate availability and climatic factors

Fungi found in Mediterranean and North Sea sponges : How specific are they?

Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twentytwo of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point in the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community

Reconstructing functional networks in the human intestinal tract using synthetic microbiomes : Systems Biology • Nanobiotechnology

The human intestinal tract harbors one of the most densely populated and open microbial ecosystems. The application of multi-omics approaches has provided insight into a wide array of complex interactions between the various groups of mainly anaerobic colonic microbes as well as the host-microbe dialogue. Integration of multi-omits techniques in cultivation based experiments that vary in complexity from monocultures to synthetic microbial communities identified key metabolic players in the trophic interactions as well as their ecological dynamics. A synergy between these approaches will be of utmost importance to reconstruct the functional interaction networks at the ecosystem level within the human intestinal microbiome. The improved understanding of microbiome functioning at ecosystem level will further aid in developing better predictive models and design of effective microbiome modulation strategies for health benefits.Peer reviewe

vanI : a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense

Peer reviewe

Entwicklung der Darmflora von Sauen bei wechselnden Fasergehalten in der Ration

In vitro gas production studies can be used in pig nutrition to assess the metabolic capacity of intestinal microbiota to ferment fibre. The intestinal microbiota are obtained from faeces of animals adapted to a certain diet. However, the necessary adaptation time of faecal donor animals to attain a stable microbial population whose fermentation capacity is representative for a different fibre content in the diet is largely unknown. Therefore a study was carried out where two groups of sows where either changed from a diet high in fibre to a diet low in fibre or vice versa. After the diet was changed, the large intestinal microbiota was characterized every three days during a period of 19 days with a phylogenetic microarray. The diet change led to significant changes in relative abundance of specific bacteria. Bacteroidetes increased and Bacilli decreased after the diet was changed from low to high fibre while the opposite occurred when the diet was changed from high to low fibre

Syntrophic LCFA-degraders: “bacteria that can clean soap”

Wastewaters contain substantial amounts of long-chain fatty acids (LCFA) which, when in the form of sodium salts, are what we normally call soaps. These compounds, resulting from fats' hydrolysis, can be converted to high amounts of methane. Developing new technological solutions for LCFA methanation, but also understanding the physiology and microbiology of LCFA degradation is fundamental for the bioenergy valorization of fatty wastewaters. In this work we present an overview of our results on anaerobic LCFA microbial degradation. Molecular techniques were used to investigate the structure of microbial communities present in different LCFA-degrading communities, such as continuous oleate- and palmitate-fed bioreactors and several enrichment cultures degrading these two LCFA as well. Choice of oleate and palmitate as model substrates was due to their predominance in wastewaters and to the fact that they represent mono-unsaturated and saturated LCFA, respectively. DGGE fingerprinting and sequencing evidenced the importance of syntrophic bacteria, affiliated with the Syntrophomonas genus, in the degradation of these compounds. Enrichment on oleate or palmitate resulted in distinct bacterial communities, which might be related to LCFA chain-saturation differences. A new obligately syntrophic bacterium, Syntrophomonas zehnderi, was isolated from an oleate-degrading culture. The fact that S. zehnderi can degrade a wide range of fatty-acids with different chain length (C4-C18) and is also able to use unsaturated LCFA (e.g. oleate) makes it a destined and dedicated key for the anaerobic treatment of wastewaters, in which an assembly of different fatty-acids is normally present. Genome sequencing of S. zehnderi is currently undergoing

The microbiology of conversion of long-chain fatty acids (LCFA) to biogas

Wastewaters, mainly the ones from food processing industries, contain considerable amounts of long-chain fatty acids (LCFA). These pollutant compounds, resulting from the hydrolysis of lipids, can be used as energetic resources for the production of biogas. A large amount of methane can be produced from LCFA; theoretically 1g of oleate, one of the most common LCFA found in wastewaters, can be converted to 1.01 L of methane (at standard temperature and pressure), while 1 g of glucose yields only 0.37 L methane. In its core this is a biological process, thus strongly linked to the performance and efficiency of the different microorganisms interacting in the process. Insight into the phylogenetic and functional communities involved in LCFA degradation is necessary to understand and enable the effective performance of bioreactors treating these compounds. In this work we describe the application of culture-dependent and culture-independent strategies to study microbiological and physiological aspects of the degradation of LCFA in anaerobic environments. Two LCFA were used as model substrates: oleate, a mono-unsaturated LCFA (C18:0), and palmitate, a saturated LCFA (C16:0), both abundant in LCFA-rich wastewaters. LCFA-degrading communities were developed by selective enrichments growing on oleate and palmitate. Changes in the microbial composition during enrichment were analyzed by DGGE profiling of PCR-amplified 16S rRNA gene fragments. Predominant DGGE-bands of the enrichment cultures were identified by 16S rRNA gene sequencing. A significant part of the retrieved 16S rRNA gene sequences was most similar to those of uncultured bacteria. 16S rRNA gene sequences clustering within the Syntrophomonadaceae family were identified as corresponding to predominant DGGE-bands in the oleate- and palmitateenrichment cultures. In stable palmitate-enrichment cultures members of the Syntrophobacteraceae family were also present. Further on, a new obligately syntrophic bacterium, Syntrophomonas zehnderi, was isolated from an oleate-degrading culture. This mesophilic, syntrophic, fatty acid oxidizing bacterium degrades straight-chain fatty acids with 4 to 18 carbon atoms but, also, unsaturated LCFA, such as oleate. The presence of Syntrophomonas zehnderi related bacteria in several sludges after contact with oleate was, subsequently, verified by DGGE-fingerprinting analysis and suggests its important role in anaerobic oleate degradation in bioreactor sludge. Future work on the performance of bioaugmented reactors with this versatile LCFA-degrading bacterium promise new results on the efficient conversion of LCFA to methane

Effect of a Low-Methane Diet on Performance and Microbiome in Lactating Dairy Cows Accounting for Individual Pre-Trial Methane Emissions

Simple Summary Low methane-emitting dietary ingredients have been identified in extensive research conducted during the past decade. This study investigated the effects of replacing grass silage with maize silage, with or without rapeseed oil supplementation, on the methane emissions and performance of dairy cows. Pre-trial measurements of methane-emissions were used in the evaluation. Partial replacement of grass silage with maize silage did not affect methane emissions but reduced dairy cow performance. Adding rapeseed oil to the diet substantially reduced methane emissions due to modified rumen microbiota, resulting in impaired nutrient intake, digestibility, and yield of energy-corrected milk. Correcting for individual cow characteristics of methane emissions did not affect the magnitude of suppression of methane emissions by dietary treatments. This study examined the effects of partly replacing grass silage (GS) with maize silage (MS), with or without rapeseed oil (RSO) supplementation, on methane (CH4) emissions, production performance, and rumen microbiome in the diets of lactating dairy cows. The effect of individual pre-trial CH4-emitting characteristics on dietary emissions mitigation was also examined. Twenty Nordic Red cows at 71 +/- 37.2 (mean +/- SD) days in milk were assigned to a replicated 4 x 4 Latin square design with four dietary treatments (GS, GS supplemented with RSO, GS plus MS, GS plus MS supplemented with RSO) applied in a 2 x 2 factorial arrangement. Partial replacement of GS with MS decreased the intake of dry matter (DM) and nutrients, milk production, yield of milk components, and general nutrient digestibility. Supplementation with RSO decreased the intake of DM and nutrients, energy-corrected milk yield, composition and yield of milk fat and protein, and general digestibility of nutrients, except for crude protein. Individual cow pre-trial measurements of CH4-emitting characteristics had a significant influence on gas emissions but did not alter the magnitude of CH4 emissions. Dietary RSO decreased daily CH4, yield, and intensity. It also increased the relative abundance of rumen Methanosphaera and Succinivibrionaceae and decreased that of Bifidobacteriaceae. There were no effects of dietary MS on CH4 emissions in this study, but supplementation with 41 g RSO/kg of DM reduced daily CH4 emissions from lactating dairy cows by 22.5%

Intestinal microbiome landscaping : insight in community assemblage and implications for microbial modulation strategies

High individuality, large complexity and limited understanding of the mechanisms underlying human intestinal microbiome function remain the major challenges for designing beneficial modulation strategies. Exemplified by the analysis of intestinal bacteria in a thousand Western adults, we discuss key concepts of the human intestinal microbiome landscape, i.e. the compositional and functional 'core', the presence of community types and the existence of alternative stable states. Genomic investigation of core taxa revealed functional redundancy, which is expected to stabilize the ecosystem, as well as taxa with specialized functions that have the potential to shape the microbiome landscape. The contrast between Prevotella-and Bacteroides-dominated systems has been well described. However, less known is the effect of not so abundant bacteria, for example, Dialister spp. that have been proposed to exhibit distinct bistable dynamics. Studies employing time-series analysis have highlighted the dynamical variation in the microbiome landscape with and without the effect of defined perturbations, such as the use of antibiotics or dietary changes. We incorporate ecosystem-level observations of the human intestinal microbiota and its keystone species to suggest avenues for designing microbiome modulation strategies to improve host health.Peer reviewe

Reactive Oxygen Species on the Early Earth and Survival of Bacteria

An oxygen-rich atmosphere appears to have been a prerequisite for complex, multicellular life to evolve on Earth and possibly elsewhere in the Universe. However it remains unclear how free oxygen first became available on the early Earth. A potentially important, and as yet poorly constrained pathway, is the production of oxygen through the weathering of rocks and release into the near-surface environment. Reactive Oxygen Species (ROS), as precursors to molecular oxygen, are a key step in this process, and may have had a decisive impact on the evolution of life, present and past. ROS are generated from minerals in igneous rocks during hydrolysis of peroxy defects, which consist of pairs of oxygen anions oxidized to the valence state -1 and during (bio) transformations of iron sulphide minerals. ROS are produced and consumed by intracellular and extracellular reactions of Fe, Mn, C, N, and S species. We propose that, despite an overall reducing or neutral oxidation state of the macroenvironment and the absence of free O2 in the atmosphere, organisms on the early Earth had to cope with ROS in their microenvironments. They were thus under evolutionary pressure to develop enzymatic and other defences against the potentially dangerous, even lethal effects of oxygen and its derived ROS. Conversely it appears that microorganisms learned to take advantage of the enormous reactive potential and energy gain provided by nascent oxygen. We investigate how oxygen might be released through weathering. We test microorganisms in contact with rock surfaces and iron sulphides. We model bacteria such as Deionococcus radiodurans and Desulfotomaculum, Moorella and Bacillus species for their ability to grow or survive in the presence of ROS. We examine how early Life might have adapted to oxygen