Towards to physiological status of soil microorganisms determined by RNA:dsDNA ratio

Despite soil microorganisms spend most of their lifetime in a state of dormancy, they are quickly activated by substrate input and easily switch to growth. As both the dsDNA- and RNA- contents increase during microbial growth, the RNA:dsDNA ratio reflects a promising predictor, whether the response of a microbial community to environmental changes is due to an increase in population (by dsDNA) or due to an increase in activity (by RNA). This prediction of the RNA:dsDNA ratio can be accomplished by the comparison of microbial incubation approaches with and without addition of easily available substrates. We exhibited the RNA:dsDNA ratios for four contrasting soil types during substrate-induced growth. Overall, after glucose addition, a strong increase of dsDNA and RNA contents were determined in most of the soil types during 72 h of incubation. Furthermore, we identified distinct temporal soil-specific RNA:dsDNA patterns. The dsDNA- and RNA-contents yielded 26–174 and 0.3–30 µg g-1 soil, respectively. The soil texture was strongly associated with the reduction of RNA recovery, by means of an exponential decrease of RNA-content with increasing clay content. The lower RNA recovery in virgin and arable Chernozem (>30%) compared to soil types with lower clay contents (<17% for Retisol, Luvisol and Calcisol) suggests, that the undercount of RNA yields in clayey soils biased the RNA:dsDNA ratio, and subsequently the physiological state of the microbial community is not adequately represented in soils with clay contents exceeding 30%

Microbial hotspots and hot moments in soil: Concept & review

© 2015 Elsevier Ltd. Soils are the most heterogeneous parts of the biosphere, with an extremely high differentiation of properties and processes within nano- to macroscales. The spatial and temporal heterogeneity of input of labile organics by plants creates microbial hotspots over short periods of time - the hot moments. We define microbial hotspots as small soil volumes with much faster process rates and much more intensive interactions compared to the average soil conditions. Such hotspots are found in the rhizosphere, detritusphere, biopores (including drilosphere) and on aggregate surfaces, but hotspots are frequently of mixed origin. Hot moments are short-term events or sequences of events inducing accelerated process rates as compared to the average rates. Thus, hotspots and hot moments are defined by dynamic characteristics, i.e. by process rates.For this hotspot concept we extensively reviewed and examined the localization and size of hotspots, spatial distribution and visualization approaches, transport of labile C to and from hotspots, lifetime and process intensities, with a special focus on process rates and microbial activities. The fraction of active microorganisms in hotspots is 2-20 times higher than in the bulk soil, and their specific activities (i.e. respiration, microbial growth, mineralization potential, enzyme activities, RNA/DNA ratio) may also be much higher. The duration of hot moments in the rhizosphere is limited and is controlled by the length of the input of labile organics. It can last a few hours up to a few days. In the detritusphere, however, the duration of hot moments is regulated by the output - by decomposition rates of litter - and lasts for weeks and months. Hot moments induce succession in microbial communities and intense intra- and interspecific competition affecting C use efficiency, microbial growth and turnover. The faster turnover and lower C use efficiency in hotspots counterbalances the high C inputs, leading to the absence of strong increases in C stocks. Consequently, the intensification of fluxes is much stronger than the increase of pools. Maintenance of stoichiometric ratios by accelerated microbial growth in hotspots requires additional nutrients (e.g. N and P), causing their microbial mining from soil organic matter, i.e. priming effects. Consequently, priming effects are localized in microbial hotspots and are consequences of hot moments. We estimated the contribution of the hotspots to the whole soil profile and suggested that, irrespective of their volume, the hotspots are mainly responsible for the ecologically relevant processes in soil. By this review, we raised the importance of concepts and ecological theory of distribution and functioning of microorganisms in soil

Spatial distribution and catalytic mechanisms of β-glucosidase activity at the root-soil interface

© 2016 Springer-Verlag Berlin Heidelberg We compared modifications of soil zymography, a new in situ technique to visualize enzyme activities, based on contact of fluorgenic substrate-saturated membranes with soil either through the gel layer (gel zymography) or without gel application (direct zymography). We coupled zymography with quantitative measurements of enzyme kinetics to characterize catalytic mechanisms of β-glucosidase activity at the plant-soil interface including root surface (rhizoplane), rhizosphere, and bulk soil. Direct zymography refined and focused image resolution. The area of hotspots (i.e., spots with most intensive enzyme activity) as well as color intensity ratios estimated using direct zymography exceeded by a factor of 2 the corresponding values obtained with gel zymography. As determined by direct zymography, the percentage of hotspots associated to root surfaces was 58–68 % of total hotspot area. Hotspot area comprised only 6.8 ± 0.1 % of the total area of an image and 9.0 ± 3 % of the root surface area. The intensity of β-glucosidase activity, however, was up to 20 times higher in the hotspots versus bulk soil. The contribution of rhizosphere to β-glucosidase activity of the whole image (77–82 %) was four times higher than the contribution of the root surface. Enzyme kinetic parameters indicated different enzyme systems in bulk and rhizosphere soil. Higher substrate affinity and catalytic efficiency in bulk than in rhizosphere soil suggested relative domination of microorganisms with more efficient enzyme systems in the former. Coupling direct zymography and kinetic assays enabled mapping the two-dimensional (2D) distribution of enzyme activity at the root-soil interface and estimating the catalytic properties of root-associated and soil-associated enzymes

Spatial distribution and catalytic mechanisms of β-glucosidase activity at the root-soil interface

© 2016, Springer-Verlag Berlin Heidelberg.We compared modifications of soil zymography, a new in situ technique to visualize enzyme activities, based on contact of fluorgenic substrate-saturated membranes with soil either through the gel layer (gel zymography) or without gel application (direct zymography). We coupled zymography with quantitative measurements of enzyme kinetics to characterize catalytic mechanisms of β-glucosidase activity at the plant-soil interface including root surface (rhizoplane), rhizosphere, and bulk soil. Direct zymography refined and focused image resolution. The area of hotspots (i.e., spots with most intensive enzyme activity) as well as color intensity ratios estimated using direct zymography exceeded by a factor of 2 the corresponding values obtained with gel zymography. As determined by direct zymography, the percentage of hotspots associated to root surfaces was 58–68 % of total hotspot area. Hotspot area comprised only 6.8 ± 0.1 % of the total area of an image and 9.0 ± 3 % of the root surface area. The intensity of β-glucosidase activity, however, was up to 20 times higher in the hotspots versus bulk soil. The contribution of rhizosphere to β-glucosidase activity of the whole image (77–82 %) was four times higher than the contribution of the root surface. Enzyme kinetic parameters indicated different enzyme systems in bulk and rhizosphere soil. Higher substrate affinity and catalytic efficiency in bulk than in rhizosphere soil suggested relative domination of microorganisms with more efficient enzyme systems in the former. Coupling direct zymography and kinetic assays enabled mapping the two-dimensional (2D) distribution of enzyme activity at the root-soil interface and estimating the catalytic properties of root-associated and soil-associated enzymes

Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold temperate forests

Bacteria are one of the most abundant and diverse groups of micro-organisms and mediate many critical terrestrial ecosystem processes. Despite the crucial ecological role of bacteria, our understanding of their large-scale biogeography patterns across forests, and the processes that determine these patterns lags significantly behind that of macroorganisms. Here, we evaluated the geographic distributions of bacterial diversity and their driving factors across nine latitudinal forests along a 3,700-km north–south transect in eastern China, using high-throughput 16S rRNA gene sequencing. Four of 32 phyla detected were dominant: Acidobacteria, Actinobacteria, Alphaproteobacteria and Chloroflexi (relative abundance > 5%). Significant increases in bacterial richness and phylogenetic diversity were observed for temperate forests compared with subtropical or tropical forests. The soil organic matter (SOM) mineralisation rate (SOM , an index of SOM availability) explained the largest significant variations in bacterial richness. Variation partition analysis revealed that the bacterial community structure was closely correlated with environmental variables and geographic distance, which together explained 80.5% of community variation. Among all environmental factors, climatic features (MAT and MAP) were the best predictors of the bacterial community structure, whereas soil pH and SOM emerged as the most important edaphic drivers of the bacterial community structure. Plant functional traits (community weighted means of litter N content) and diversity resulted in weak but significant correlations with the bacterial community structure. Our findings provide new evidence of bacterial biogeography patterns from tropical to cold temperate forests. Additionally, the results indicated a close linkage among soil bacterial diversity, climate and SOM decomposition, which is critical for predicting continental-scale responses under future climate change scenarios and promoting sustainable forest ecosystem services. A plain language summary is available for this article. min mi

Interactive priming effect of labile carbon and crop residues on SOM depends on residue decomposition stage: Three-source partitioning to evaluate mechanisms

© 2018 Elsevier Ltd Inputs of crop residues and labile C (e.g. root exudates) can affect the decomposition rate of soil organic matter (SOM) through the priming effect (PE). Most previous priming studies describe the addition of single labile or residue C, ignoring the interactions of labile C and fresh or decaying crop residues commonly present in field conditions. Using a dual 13C/14C labelling approach in a 62-day incubation, we investigated the effects of adding labile C (40 μg glucose-C g−1 soil) together with wheat shoot or root residues (3.1 mg C g−1 soil) on SOM priming at three residue decomposition stages: intensive (day-1), reduced (day-9) and stabilised (day-24). To estimate the PE, total soil CO2 efflux and microbial biomass were partitioned for three sources: labile C (14C-glucose), plant residues (13C-labelled) and SOM (unlabelled). Without glucose, roots were decomposed less than shoots but induced 1.4-fold stronger cumulative SOM priming (365 μg C g−1 soil) than shoots. Addition of glucose increased SOM priming, with a stronger effect in the presence of shoot than root residues. Glucose addition at the intensive stage of shoots decomposition slightly increased SOM priming. However, compared with residues alone PE, the addition of glucose during reduced residue decomposition stage, increased SOM priming by 60% (roots) to 104% (shoots). Remarkably, this SOM priming after glucose addition was followed by a decline in residue decomposition and by an increase (up to 50%) in SOM-derived C in microbial biomass. Hence, following glucose addition, microorganisms utilised more SOM rather than feeding on decaying residues during reduced decomposition stage. During stabilised residue decomposition stage, the impact of glucose on SOM priming declined again, while the residue decomposition rate remained unaffected. Furthermore, a large proportion of added glucose (up to 10%) was retained in microbial biomass and its mineralisation rate declined strongly (compared with intensive and reduced decomposition stage). Therefore, the glucose amount was not sufficient to influence microbial activities determining SOM or stabilised residue decomposition rates. Overall, SOM decomposition increased by 1- to 4-fold more than the amount of added glucose C, which resulted in a negative net soil C balance compared with residues alone. Thus, we demonstrated for the first time that 1) the interactive effects of glucose (trace amount) and residues on SOM priming depend on plant residue type (higher under shoots than roots) and 2) stage of residues decomposition (higher SOM priming when labile C was added after the end of intensive decomposition stage of plant residues)

Analysis of microbial populations in plastic-soil systems after exposure to high poly(butylene succinate-co-adipate) load using high-resolution molecular technique

BACKGROUND: Bio-based and biodegradable plastics are considered as plastics of the future owing to their ability to decompose under various environmental conditions. However, their effects on the soil microbiome are poorly characterised. In this study, we aimed to investigate the effects of an important bio-based and biodegradable plastic, polybutylene succinate-co-adipate (PBSA), on soil microbial diversity and community composition using high-resolution molecular technique (Illumina sequencing) targeting all three microbial domains: archaea, bacteria, and fungi. RESULTS: Adding high load of PBSA to soil (6% (w/w)) caused a significant decline in archaeal (13%) and fungal (45%) richness and substantial changes in both bacterial (Proteobacteria, Actinobacteria, and Acidobacteria) and fungal (Eurotiomycetes, Sordariomycetes, Leotiomycetes, and Dothideomycetes) community composition compared with no PBSA addition to soil. The combined effects of PBSA and (NH₄)₂SO₄ fertilisation on the soil microbiome were much greater than the effects of PBSA alone. We only detected opportunistic human pathogens in low abundance on PBSA and in the surrounding soil. However, some plant pathogenic fungi were detected and/or enriched on the PBSA films and in surrounding soil. Apart from plant pathogens, many potential microbial control agents and plant growth-promoting microorganisms were also detected/enriched owing to PBSA addition. Adding high load of PBSA together with (NH₄)₂SO₄ fertilisation can either eliminate some plant pathogens or enrich specific pathogens, especially Fusarium solani, which is economically important. CONCLUSIONS: We conclude that high load of bio-based and biodegradable PBSA plastic may negatively affect soil microbiome

Carbon sequestration and turnover in soil under the energy crop Miscanthus: Repeated ¹³C natural abundance approach and literature synthesis

© 2017 John Wiley & Sons Ltd. The stability and turnover of soil organic matter (SOM) are a very important but poorly understood part of carbon (C) cycling. Conversion of C 3 grassland to the C 4 energy crop Miscanthus provides an ideal opportunity to quantify medium-term SOM dynamics without disturbance (e.g., plowing), due to the natural shift in the δ 13 C signature of soil C. For the first time, we used a repeated 13 C natural abundance approach to measure C turnover in a loamy Gleyic Cambisol after 9 and 21 years of Miscanthus cultivation. This is the longest C 3 -C 4 vegetation change study on C turnover in soil under energy crops. SOM stocks under Miscanthus and reference grassland were similar down to 1 m depth. However, both increased between 9 and 21 years from 105 to 140 mg C ha -1 (P 9 years) increased with depth from 19 years (0-10 cm) to 30-152 years (10-50 cm), and remained stable below 50 cm. From 41 literature observations, the average SOM increase after conversion from cropland or grassland to Miscanthus was 6.4 and 0.4 mg C ha -1 , respectively. The MRT of total C in topsoil under Miscanthus remained stable at ~60 years, independent of plantation age, corroborating the idea that C dynamics are dominated by recycling processes rather than by C stabilization. In conclusion, growing Miscanthus on C-poor arable soils caused immediate C sequestration because of higher C input and decreased SOM decomposition. However, after replacing grasslands with Miscanthus, SOM stocks remained stable and the MRT of old C 3 -C increased strongly with depth

Oily waste containing natural radionuclides: Does it cause stimulation or inhibition of soil bacterial community?

© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Contamination with oily wastes containing natural radionuclides is a potential hazard for soil health and function. Our study aimed to reveal both structural and functional changes of the microbial community resistant to and able to decompose oily wastes in soil. To do this, we determined CO2 efflux, microbial biomass (by the extraction-fumigation method), and community structure (by PCR-SSCP) for 120 d after application of radioactive oily wastes to the soil at the ratio 1:4. The addition of the waste resulted in an increase of the activity concentration of 226Ra by 130 times (up to 643 Bq kg-1) and of 232Th by 29 times (up to 254 Bq kg-1). The calculated weighted dose for the radionuclide 226Ra was found to be below the values that are known to affect microorganisms. However, the cumulative effect of a repeated deposition of radioactive oily waste may result in an increase of the weighted dose up to an effective level. During the incubation, the hydrocarbon (HC) content of the waste-treated soil decreased from 156 to 54 g kg-1 of soil indicating intensive decomposition of added organics by soil microorganisms. The waste application, however, led to an inhibition of soil microbial biomass compared with the control (by 26-47%). Microbial respiration was stimulated in the first month of incubation and then decreased until the end of the incubation period (by up to 74% compared to the control). The qCO2 was estimated to be 3-fold higher than the control on day 1 of incubation and equal to the control on day 120 of incubation. The bacterial diversity decreased in the contaminated soil compared with the control soil. The bacterial community structure was altered by domination of new oil degrader species belonging to the genera Dyella, Pseudoxanthomonas, Sinobacter, and Parvibaculum. Thus, disposal of radioactive petroleum waste strongly altered the structure of the microbial community resulting in the selection of resistant species able to decompose pollutants and also affected the community function (inhibition of microbial biomass and stimulation of respiration) which tended to stabilize after long-term incubation