Effects of stand age and soil organic matter quality on soil bacterial and fungal community composition in Larix gmelinii plantations, Northeast China

It is of great interest to elucidate the biogeographic patterns of soil microorganisms and their driving forces, which is fundamental to predicting alterations in microbial-mediated functions arising from environment changes. Although the vertical movement of dissolved organic matter (DOM) drives the cycle of nutrients such as soil carbon but, in the restored ecosystem, the relationship between DOM and soil microbial nutrient utilization remains to be determined. Here, we investigated the changes of soil microbial community at 0-40 cm depth profile in three stages (10-, 30-, 50-years) of succession in Larix olgensis plantations and the fluorescence spectrum composition of DOM. With the increase of soil depth, the signal source of microorganisms increases. In a coniferous forest soil environment, the possible main source of DOM in deep soil is the production of microbial metabolism. Difficulty in the decomposition of organic matter determines the distribution and composition of microorganisms. Increasing forest age makes bacteria and fungi more specific and bacterial-fungal associations greater. Overall, our work contributes to the understanding of factors underlying microbial community distribution in plantation forests and the importance of DOM quality in building microbial communities.

The importance of allochthonous organic matter quality when investigating pulse disturbance events in freshwater lakes: a mesocosm experiment

Extreme precipitation is occurring with greater frequency and intensity as a result of climate change. Such events boost the transport of allochthonous organic matter (allo-OM) to freshwater ecosystems, yet little is known about the impacts on dissolved organic matter (DOM) quality and seston elemental stoichiometry, especially for lakes in warm climates. A mesocosm experiment located in a Turkish freshwater lake was designed to simulate a pulse event leading to increased inputs of allo-OM by examining the individual effects of increasing water colour (HuminFeed®, HF), the direct effects of the extra energetic inputs (alder tree leaf leachate, L), and the interactions of the single treatment effects (combination of both sources, HFL), along with a comparison with unmanipulated controls. Changes in the DOM quality and nutrient stoichiometry of the allo-OM treatment additions was examined over the course of the experiments. Results indicated that there was an increase of high recalcitrant DOM components in the HF treatment, in contrast to an increase in less aromatic microbially derived molecules for the L treatment. Unexpectedly, seston C:P ratios remained below a severe P-limiting threshold for plankton growth and showed the same temporal pattern in all mesocosms. In contrast, seston N:P ratios differed significantly between treatments, with the L treatment reducing P-limiting conditions, whilst the HF treatment increased them. The effects of the combined HFL treatment indicated an additive type of interaction and chlorophyll-a was highest in the HFL treatment. Our results demonstrate that accounting for the optical and stoichiometric properties of experimental allo-OM treatments is crucial to improve the capacity to explain extrapolated conclusions regarding the effects of climate driven flooding on freshwater ecosystems in response to global climate change. Graphical abstract

Application of the D-A-(C) index as a simple tool for microbial-ecological characterization and assessment of groundwater ecosystems—a case study of the Mur River Valley, Austria

The assessment and monitoring of the ecological quality and status of groundwater is a timely issue. At present, various assessment tools have been developed that now await application and validation. One of these, the D‑A‑C index, evaluates the microbiological-ecological quality of groundwater based on of prokaryotic cell counts, microbial activity measurements, and the qualitative characterization of dissolved organic carbon (DOM). The purpose of this paper is to illustrate the different ways of application of the D‑A-(C) index making use of a recently collected data set (n = 61) from the river Mur valley, Austria. First, we present an extension of the D‑A-(C) index by including measurements of dissolved organic matter quality (DOM) derived from fluorescence spectroscopy as additional variables to supplement the analysis of microbial cell density and activity levels. Second, we illustrate how the definition of a reference status for a ‘good’ microbiological-ecological state can improve the analysis and allow for a more sensitive and accurate detection of impacts on groundwater ecosystems. Based on our results, we advocate that the analysis be performed by making use of expert knowledge for the definition of reference sites to which target sites are to be compared.

Vertical Niche Partitioning of Archaea and Bacteria Linked to Shifts in Dissolved Organic Matter Quality and Hydrography in North Atlantic Waters

Understanding the factors that modulate prokaryotic assemblages and their niche partitioning in marine environments is a longstanding challenge in marine microbial ecology. This study analyzes amplicon sequence variant (ASV) diversity and co-occurrence of prokaryotic (Archaea and Bacteria) communities through coastal-oceanic gradients in the NW Iberian upwelling system and adjacent open-ocean (Atlantic Ocean). Biogeographic patterns were investigated in relation with environmental conditions, mainly focusing on the optical signature of the dissolved organic matter (DOM). Alpha- and beta-diversity were horizontally homogeneous [with the only exception of Archaea (∼1700 m depth), attributed to the influence of Mediterranean water, MW], while beta-diversity was significantly vertically stratified. Prokaryotic communities were structured in four clusters (upper subsurface, lower subsurface, intermediate, and deep clusters). Deep (>2000 m) archaeal and bacterial assemblages, and intermediate (500-2000 m) Bacteria (mainly SAR202 and SAR406), were significantly related to humic-like DOM (FDOM-M), while intermediate Archaea were additionally related to biogeochemical attributes of the high-salinity signature of MW. Lower subsurface (100-500 m) Archaea (particularly one ASV belonging to the genus Candidatus Nitrosopelagicus) were mainly related to the imprint of high-salinity MW, while upper subsurface (≤100 m) archaeal assemblages (particularly some ASVs belonging to Marine Group II) were linked to protein-like DOM (aCDOM254). Conversely, both upper and lower subsurface bacterial assemblages were mainly linked to aCDOM254 (particularly ASVs belonging to Rhodobacteraceae, Cyanobacteria, and Flavobacteriaceae) and nitrite concentration (mainly members of Planctomycetes). Most importantly, our analysis unveiled depth-ecotypes, such as the ASVs MarG.II_1 belonging to the archaeal deep cluster (linked to FDOM-M) and MarG.II_2 belonging to the upper subsurface cluster (related to FDOM-T and aCDOM254). This result strongly suggests DOM-mediated vertical niche differentiation, with further implications for ecosystem functioning. Similarly, positive and negative co-occurrence relationships also suggested niche partitioning (e.g., between the closely related ASVs Thaum._Nit._Nit._Nit._1 and _2) and competitive exclusion (e.g., between Thaum._Nit._Nit._Nit._4 and _5), supporting the finding of non-randomly, vertically structured prokaryotic communities. Overall, differences between Archaea and Bacteria and among closely related ASVs were revealed in their preferential relationship with compositional changes in the DOM pool and environmental forcing. Our results provide new insights on the ecological processes shaping prokaryotic assembly and biogeography.

Shifts in the Abundances of Saprotrophic and Ectomycorrhizal Fungi With Altered Leaf Litter Inputs

Ectomycorrhizal (EcM) and saprotrophic fungi interact in the breakdown of organic matter, but the mechanisms underlying the EcM role on organic matter decomposition are not totally clear. We hypothesized that the ecological relations between EcM and saprotroph fungi are modulated by resources availability and accessibility, determining decomposition rates. We manipulated the amount of leaf litter inputs (No-Litter, Control Litter, Doubled Litter) on Trenched (root exclusion) and Non-Trenched plots (with roots) in a temperate deciduous forest of EcM-associated trees. Resultant shifts in soil fungal communities were determined by phospholipid fatty acids and DNA sequencing after 3 years, and CO2 fluxes were measured throughout this period. Different levels of leaf litter inputs generated a gradient of organic substrate availability and accessibility, altering the composition and ecological relations between EcM and saprotroph fungal communities. EcM fungi dominated at low levels of fresh organic substrates and lower organic matter quality, where short-distances exploration types seem to be better competitors, whereas saprotrophs and longer exploration types of EcM fungi tended to dominate at high levels of leaf litter inputs, where labile organic substrates were easily accessible. We were, however, not able to detect unequivocal signs of competition between these fungal groups for common resources. These results point to the relevance of substrate quality and availability as key factors determining the role of EcM and saprotroph fungi on litter and soil organic matter decay and represent a path forward on the capacity of organic matter decomposition of different exploration types of EcM fungi.

Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile

Permafrost peatlands, containing a sizable amount of soil organic carbon (OC), play a pivotal role in soil (peat) OC transformation into soluble and volatile forms and greatly contribute to overall natural CO2 and CH4 emissions to the atmosphere under ongoing permafrost thaw and soil OC degradation. Peat microorganisms are largely responsible for the processing of this OC, yet coupled studies of chemical and bacterial parameters in permafrost peatlands are rather limited and geographically biased. Towards testing the possible impact of peat and peat pore water chemical composition on microbial population and diversity, here we present results of a preliminary study of the western Siberia permafrost peatland discontinuous permafrost zone. The quantitative evaluation of microorganisms and determination of microbial diversity along a 100 cm thick peat soil column, which included thawed and frozen peat and bottom mineral horizon, was performed by RT-PCR and 16S rRNA gene-based metagenomic analysis, respectively. Bacteria (mainly Proteobacteria, Acidobacteria, Actinobacteria) strongly dominated the microbial diversity (99% sequences), with a negligible proportion of archaea (0.3–0.5%). There was a systematic evolution of main taxa according to depth, with a maximum of 65% (Acidobacteria) encountered in the active layer, or permafrost boundary (50–60 cm). We also measured C, N, nutrients and ~50 major and trace elements in peat (19 samples) as well as its pore water and dispersed ice (10 samples), sampled over the same core, and we analyzed organic matter quality in six organic and one mineral horizon of this core. Using multiparametric statistics (PCA), we tested the links between the total microbial number and 16S rRNA diversity and chemical composition of both the solid and fluid phase harboring the microorganisms. Under climate warming and permafrost thaw, one can expect a downward movement of the layer of maximal genetic diversity following the active layer thickening. Given a one to two orders of magnitude higher microbial number in the upper (thawed) layers compared to bottom (frozen) layers, an additional 50 cm of peat thawing in western Siberia may sizably increase the total microbial population and biodiversity of active cells.

Properties of humic acids depending on the land use in different parts of Slovakia

Many studies report organic carbon stabilization by clay minerals, but the effects of land use and soil type on the properties of humic acids (HAs) are missing. The aim of the paper is to determine the effects of land use and soil types on the characteristics of HAs, which have a considerable influence on organic matter quality. It was hypothesised that the effect of the land use on HAs properties depends on the particular size distribution. The research was performed in three ecosystems: agricultural, forest, and meadow, located in Slovakia. From each of them, the samples of 4 soil types were taken: Chernozem, Luvisol, Planosol, and Cambisol. The soil samples were assayed for the content of total organic carbon (TOC) and the particle size distribution. HAs were extracted with the Schnitzer method and analysed for the elemental composition, spectrometric parameters in the UV-VIS range, and hydrophilic and hydrophobic properties, and the infrared spectra were produced. The research results have shown that the properties of HAs can be modified by the land use and the scope and that the direction of changes depends on the soil type. The HAs of Chernozem and Luvisol in the agri-ecosystem were identified with a higher “degree of maturity”, as reflected by atomic ratios (H/C, O/C, O/H), absorbance coefficients, and the FT-IR spectra, as compared with the HAs of the meadow and forest ecosystem. However, as for the HAs of Cambisol, a higher “degree of maturity” was demonstrated for the meadow ecosystem, as compared with the HAs of the agri- and forest ecosystem. The present research has clearly identified that the content of clay is the factor determining the HAs properties. Soils with a higher content of the clay fraction contain HAs with a higher “degree of maturity”.