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Substantial amounts of organic matter are mobilized from upper soil layers during extreme precipitation events. This results in considerable fluxes of carbon from plant-associated topsoil to deeper mineral soil and to groundwater. Microbes constitute an important part of this mobile organic matter (MOM) pool. Previous work has shown that specific bacteria associated with the rhizosphere of decaying maize roots were selectively transported with seepage water upon snowmelt in winter. However, effective mechanisms of mobilization and also possible distinctions to microbial transport for living root systems remain poorly understood. In the present study, bacteria in seepage water were sampled from lysimeters at an experimental maize field after extreme rain events in summer. We show that a distinctive subset of rhizoplane-associated bacterial populations was mobilized after summer rain, especially including abundant members of the Bacteroidetes , representing a microbial conduit for fresh plant-derived carbon inputs into deeper soil layers. Marked distinctions of seepage communities were not observed between lysimeters with a different relative contribution of preferential vs. matrix flow. Time-resolved analyses of seepage water during an artificial rain event revealed temporal patterns in the mobilization of certain lineages, with members of the Chitinophagaceae , Sphingomonadaceae , and Bradyrhizobiaceae preferentially mobilized in early and late seepage fractions, and members of the candidate phyla Parcubacteria and Microgenomates mobilized mostly in intermediate fractions. While average bacterial cell counts were at ∼10 7  ml −1 in seepage water, the recovery of amended fluorescently labeled cells of Arthrobacter globiformis was low (0.2–0.6%) over seepage events. Still, mobilized bacteria clearly have the potential to influence bacterial activities and communities in subsoils. These findings demonstrate that dynamic hydraulic events must be considered for a better understanding of the connectivities between microbial populations and communities in soil, as well as of the links between distinct carbon pools over depth. [ABSTRACT FROM AUTHOR]

Stable isotope probing of RNA has enthused researchers right from its first introduction in 2002. The concept of a labelling-based detection of process-targeted microbes independent of cellular replication or growth has allowed for a much more direct handle on functionally relevant microbiota than by labelling of other biomarkers. This has led to a widespread application of the technology, and breakthroughs in our understanding of carbon flow in natural microbiomes, autotrophic and heterotrophic physiologies, microbial food webs, host–microbe interactions and environmental biotechnology. Recent studies detecting labelled mRNA demonstrate that RNA-SIP is not limited to the analysis of rRNA, but is currently developing towards an approach for accessing targeted transcriptomes. In combination with next-generation sequencing and other methodological advances, RNA-SIP will continue to deliver invaluable insights into the functioning of microbial communities. [ABSTRACT FROM AUTHOR]

The hyporheic interstitial provides habitat for many different organisms – from bacteria to burrowing invertebrates. Due to their burrowing and sediment reworking behaviour, these ecosystem engineers have the potential to affect hyporheic processes such as respiration and nutrient cycling. However, there is a lack of studies that characterize the interactions between bioturbators, physico-chemical habitat properties and microbial communities in freshwater substrates. In a standardized laboratory experiment, we investigated the effects of three functionally different bioturbators, duck mussels ( Anodonta anatina , Linnaeus 1758), mayfly nymphs ( Ephemera danica , Müller 1764) and tubificid worms ( Tubifex tubifex , Müller 1774), on the physico-chemical conditions and bacterial communities in hyporheic substrates. We hypothesized that different invertebrates distinctly alter habitat conditions and thus microbial community composition, depending on the depth and the manner of burrowing. A. anatina and E. danica caused an increase in interstitial oxygen concentration, whereas strong declines in oxygen concentration and redox potential were detected in the T. tubifex treatment. These effects on physico-chemical habitat properties were even detectable in open water. Mussels and tubificid worms also significantly influenced the composition of bacterial communities in the hyporheic zone. A loss or replacement of bioturbators in stream ecosystems due to anthropogenic habitat alterations is expected to result in shifts in microbial community compositions, with effects on nutrient fluxes, pollutant degradation and benthic food webs. An understanding of the effects of functionally different native and invasive bioturbators is crucial to predict changes in stream ecosystem functioning. [ABSTRACT FROM AUTHOR]

Abstract: Hyporheic substrates play a key role in aquatic ecosystems, and increasing loads of fine sediment are considered one of the major threats to stream ecosystems. Knowledge concerning the interaction of stream substratum properties with habitat quality and microbial community structure is essential for a comprehensive understanding of the functionality of the hyporheic zone. To date, there is a lack of optimal field sampling methods for hyporheic microbial communities in streams. We systematically tested the effects of defined substratum textures on the physicochemical properties of interstitial water and on bacterial communities utilising T-RFLP fingerprinting. We also tested the representativeness of different methodological approaches of investigating bacterial diversity comparing sampling of substratum, interstitial water, and exposed coupons made of granite, carbonate and glass. The temporal development of physicochemical habitat characteristics in the interstitial zone, especially of fish-toxic nitrogen compounds and oxygen supply, significantly depended on substratum texture and was strongly correlated with bacterial community composition. Multivariate analyses of bacterial community data indicated strong differences in community composition between direct (substratum samples) and indirect (interstitial water samples, coupons) sampling strategies. Substratum samples yielded highest richness of operational taxonomic units (OTUs) and the most pronounced temporal dynamics of bacterial community composition. Consequently, this technique appears most representative for assessing bacterial community structure and diversity in hyporheic habitats. The observed couplings between substratum texture, physicochemical habitat conditions and bacterial community structure expand current knowledge of previously described negative effects of fine sediments on taxa from higher levels of biological organization. [Copyright &y& Elsevier]

Abstract: Due to the scarcity or complete absence of higher organisms, protists may represent an important higher trophic level (above Prokaryotes) in the food webs of groundwater habitats. Nevertheless, the importance of aquifer protists, especially in contaminated groundwater environments, is poorly understood. Partly, this may be due to a lack of adequate PCR and fingerprinting approaches for protists in aquifers, which can be considered low in protistan or high in non-target rRNA gene copy numbers. Therefore, we have validated the suitability of distinct eukaryote-targeted primer pairs and restriction endonucleases for T-RFLP fingerprinting of protistan communities. By in silico predictions, and by fingerprinting, cloning and sequencing of microeukaryote amplicons from hydrocarbon-contaminated aquifer sediment DNA, we show that the Euk20f/Euk516r primer set in combination with Bsh1236I digestion is best suited for the recovery of diverse protistan 18S rRNA lineages. In contrast to other tested primer sets, a preferred recovery of fungal and archaeal non-target amplicons was not observed. In summary, we present an optimised microeukaryote-targeted PCR/T-RFLP fingerprinting approach which may be of value for the characterisation of protistan communities in groundwater and other habitats. [Copyright &y& Elsevier]

Plants introduce abundant carbon into soils, where it is mineralised and sequestered. Proportions of this fresh organic carbon introduced to top soils can be relocated to deeper soil layers and even to groundwater by event-driven transport upon heavy rainfalls or after snowmelt. It is assumed that a significant fraction of this flux involves biocolloids and possibly microbial biomass itself. However, the nature of such transported microbes, their origin and the mechanisms of their mobilisation are still poorly understood. Here, we provide primary evidence that specific microbial populations are exported from top soils upon seepage events. At an experimental maize field, we have analysed the composition of mobilised bacterial communities collected in seepage water directly after snowmelt in winter at different depths (35 and 65 cm), and compared them to the corresponding bulk soil microbiota. Using T-RFLP fingerprinting and pyrotag sequencing, we reveal that mostly members of the Betaproteobacteria (Methylophilaceae, Oxalobacteraceae, Comamonadaceae), the Alphaproteobacteria (Sphingomonadaceae, Bradyrhizobiaceae), the Gammaproteobacteria (Legionellaceae) and the Bacteroidetes (Sphingobacteriaceae) were mobilised, all characteristic taxa for the rhizoplane. This highlights the importance of preferential flow along root channels for the vertical mobilisation and transport of microbes. Although the estimated quantitative fluxes of bacterial biomass carbon appeared low, our study allows for an improved understanding of the links between top soil, subsoil, and groundwater microbiota, as well as carbon fluxes between soil compartments. [ABSTRACT FROM AUTHOR]

Microbial ecologists have long sought to associate the transformation of compounds in the environment with the microbial clades responsible. The development of stable isotope probing (SIP) has made this possible in many ecological and biotechnological contexts. RNA-based SIP technologies represent a significant leap forward for culture-independent ‘functional phylogeny’ analyses, where specific consumption of a given compound carrying a 13C signature can be associated with the small subunit ribosomal RNA molecules of the microbes that consume it. Recent advances have led to the unequivocal identification of microorganisms responsible for contaminant degradation in engineered systems, and to applications enhancing our understanding of carbon flow in terrestrial ecosystems. [Copyright &y& Elsevier]

Abstract Numerous 13CO 2 labeling studies have traced the flow of carbon from fresh plant exudates into rhizosphere bacterial communities. However, the succession of the uptake of carbon leaving the roots by distinct rhizosphere microbiota has rarely been resolved between microbial kingdoms. This can provide valuable insights on the niche partitioning of primary rhizodeposit consumption, as well as on community interactions in plant-derived carbon flows in soil. Here, we have traced the flow of fresh plant assimilates to rhizosphere microbiota of maize (Zea mays L.) by rRNA-stable isotope probing (SIP). Carbon flows involving bacteria, unicellular fungi, as well as protists were observed over 5 and 8 days. Surprisingly, labeling of Paraglomerales and several bacteria including Opitutus, Mucliaginibacter and Massilia spp. was especially apparent in soil surrounding the strict rhizosphere after 5 d. This highlights the central role of arbuscular mycorrhizal fungi (AMF) as a shunt for fresh plant assimilates to soil microbes not directly influenced by root exudation. Distinct trophic webs involving different flagellates, amoeba and ciliates were also observed in rhizosphere and surrounding soil, while labeling of filamentous saprotrophic Ascomycota or Basidiomycota was not apparent. This challenges the proposed "sapro-rhizosphere" concept and demonstrates the utility of rRNA-SIP to disentangle inter-kingdom microbial relationships in the rhizosphere. Graphical abstract Image 1 Highlights • rRNA-SIP was used to trace plant-derived carbon flows in the rhizosphere of maize. • 13C-labeling of mycorrhiza was stronger in surrounding soil than in the rhizosphere. • Labelling of bacteria incl. Opitutus spp. was also stronger in surrounding soil. • AMF are a shunt of plant assimilates to microbes outside the strict rhizosphere. [ABSTRACT FROM AUTHOR]

• Bidirectional water fluxes affect streambed microbial community assembly. • Interactions between N- and S-cycles stimulated by bidirectional water exchange. • Full-length amplicon sequencing of streambed microbiomes. • Sulfuricurvum spp. and Thiobacillus spp. are prominent taxa. • Agricultural lower-order streams are not only drainage channels, but reactors. The input of nitrate and other agricultural pollutants in higher-order streams largely derives from first-order streams. The streambed as the transition zone between groundwater and stream water has a decisive impact on the attenuation of such pollutants. This reactivity is not yet well understood for lower-order agricultural streams, which are often anthropogenically altered and lack the streambed complexity allowing for extensive hyporheic exchange. Reactive hot spots in such streambeds have been hypothesized as a function of hydrology, which controls the local gaining (groundwater exfiltration) or losing (infiltration) of stream water. However, streambed microbial communities and activities associated with such reactive zones remain mostly uncharted. In this study, sediments of a first-order agriculturally impacted stream in southern Germany were investigated. Along with a hydraulic dissection of distinct gaining and losing reaches of the stream, community composition and the abundance of bacterial communities in the streambed were investigated using PacBio long-read sequencing of bacterial 16S rRNA gene amplicons, and qPCR of bacterial 16S rRNA and denitrification genes (nirK and nirS). We show that bidirectional water exchange between groundwater and the stream represents an important control for sediment microbiota, especially for nitrate-reducing populations. Typical heterotrophic denitrifiers were most abundant in a midstream net losing section, while up- and downstream net gaining sections were associated with an enrichment of sulfur-oxidizing potential nitrate reducers affiliated with Sulfuricurvum and Thiobacillus spp. Dispersal-based community assembly was found to dominate such spots of groundwater exfiltration. Our results indicate a coupling of N- and S-cycling processes in the streambed of an agricultural first-order stream, and a prominent control of microbiology by hydrology and hydrochemistry in situ. Such detailed local heterogeneities in exchange fluxes and streambed microbiomes have not been reported to date, but seem relevant for understanding the reactivity of lower-order streams. Graphical Abstract [Display omitted]. [ABSTRACT FROM AUTHOR]

Introduction of glyphosate-resistant soybean plants into agricultural systems has greatly increased the application frequency of glyphosate. Because glyphosate is able to inhibit 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) not only in plants but also in different microorganisms, its application could lead to shifts in rhizosphere microbial communities in farming soils. In this study, greenhouse experiments were conducted with the objective to evaluate the effects of glyphosate on the composition and diversity of rhizosphere bacterial communities of transgenic soybean. This was especially relevant, because foliar applied glyphosate is transported down to the roots and exuded into the rhizosphere. After two foliar herbicide applications, root samples of treated and untreated plants were analysed by 16S rRNA gene T-RFLP analysis. Multivariate statistical analysis of the data and diversity indices were used to assess changes in the microbial populations in response to glyphosate applications. A comparison of rhizosphere communities revealed that the abundance of a T-RF representing microbes related to Burkholderia sp. significantly decreased under glyphosate application, while the abundance of a T-RF representing uncultured Gemmatimonadetes significantly increased. Interestingly, the bacterial community associated with soybean roots after glyphosate application not only demonstrated effective resilience after the disturbance but in addition, T-RF diversity also increased in comparison to the untreated control samples. The results suggest that bacterial diversity was even stimulated in the rhizosphere after glyphosate application. [ABSTRACT FROM AUTHOR]

Abstract: Soil food webs are important determinants for the carbon flow through terrestrial systems, with the trophic networks between microbes and microfaunal grazers forming the basis for processing plant resources. At an agricultural field site cropped with maize or wheat, plant carbon input to soil was experimentally manipulated by amendment with maize litter. The community structure of dominant micro-food web components, the bacteria, fungi, protozoa and nematodes, was investigated across a depth gradient comprising plough layer, rooted soil below plough horizon, and deeper root free soil. The community composition and diversity within micro-food webs, and the response to resource supply, were assessed in summer, the vegetation period with highest root exudation. In the plough layer amendment with plant residues increased microbial biomass as well as density of fan shaped amoeba morphotypes and of bacterial- and fungal-feeding nematodes. Diversity of food web assemblages was assessed by operational taxonomic units (OTU) for bacteria and fungi, protozoa morphotypes and nematode families. Changes in diversity were either not apparent (fungi, protozoa), negatively related to litter (bacteria) or positively linked to the presence of a specific crop plant (bacteria, nematodes). Based on nematode functional guilds and the related enrichment and structure index, general food web conditions were assigned as nutrient enriched, with a high degree of disturbance, and a dominance of the bacterial energy channel. In sum, litter amendment fostered the abundance but not the diversity of organisms as food webs remained bottom heavy with only small amounts of carbon conserved at higher trophic levels. Food web structure was more affected by the abiotic (soil profile) and biotic (crop plant) environment than by the supply with litter resources. [Copyright &y& Elsevier]