Higher Microbial Biomass Research Articles

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.

As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples. We find that these methods are important for obtaining accurate results in low biomass samples (e.g., tissue, skin). Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.

Perennial crops shape the soil microbial community and increase the soil carbon in the upper soil layer

Soil biodiversity is threatened by intensive agriculture that relies on annual grain crop production, thus leading to a decline in soil functions and ecosystem services. Perennial grain crops have a positive impact on the soil microbial community, but the responsive microbial groups and the magnitude of their response remain uncertain. To elucidate this, we analysed soil microbial biomass and community composition, bacterial growth and soil total carbon in five crops: organic perennial intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®), organic IWG-alfalfa intercrop, organic biennial grass-legume mixture, organic annual wheat or rye and conventional annual wheat. The analysis was carried out at three time points under two growing seasons at four different soil depths. Five years after establishment, IWG had greater amounts of soil total fungi and bacteria, and of arbuscular mycorrhizal (AM) fungi, saprotrophic fungi, gram-negative (G−) and gram-positive (G+) bacteria compared to annual wheat. Crop perenniality influenced the soil microbial community structure although precipitation, soil temperature and water content were the main drivers of the patterns of and temporal variations in the microbial community. Perennial crops, with reduced tillage and low nitrogen input management increased the proportions of fungi relative to bacteria, AM fungi to saprotrophic fungi, G− bacteria to G+ bacteria, and the growth rate of total bacteria. This resulted in a more active soil microbial community with higher microbial biomass than annual wheat and contributed to the increased soil total carbon storage in the 0–5 cm soil layer in a humid continental climate. The findings emphasize the importance of combining a no tillage strategy with long-term vegetation cover to increase soil quality.

Miscanthus litter additions induce a successional change in the soil micro-food web with apparent decreases in soil nitrogen

The rapid loss of soil carbon (C) from cultivated peatland soils is leading to the use of high lignin, C-rich litter amendments as a potential solution to slow C losses. These chemically recalcitrant litter inputs are expected to cause microbial nitrogen (N) immobilization as a result of changes in the soil micro-food web, but whether bioavailable N is altered by litter as it is decomposed by the micro-food web remains unclear. We monitored changes in the soil nematode, fungal, and bacterial communities over time and across space (the rhizosphere and bulk soil) after field-applying different types of ligneous litter from miscanthus, ash, willow, or larch to a cultivated peatland soil. We found that miscanthus grass (C:N = 118) induced succession from fast-growing nematodes (cp-1) to slower-growing, cp-3 and cp-4 nematodes and this corresponded to reduced N availability. This lower soil N was likely due to relatively higher microbial biomass we observed with miscanthus, combined with a decrease in fast-growing bacterivores, limiting N mineralization from nematode grazing. We did not observe strong effects on the soil micro-food web or microbial biomass N for the other woody litters that had much higher C:N. This indicates that the changes in nematode community composition following ligneous litter inputs and subsequent impacts on soil N depend on litter type but are independent of litter C:N. Miscanthus amendments also corresponded to the lowest lettuce yield of all the amendments and thus caution is raised when using miscanthus straw as a widely-applied litter. Our results provide a useful reference to predict the effect of litter amendments on cultivated peatland soils through soil micro-food web dynamics, and bioavailable N for the crop.

Significant Differences in Microbial Soil Properties, Stoichiometry and Tree Growth Occurred within 15 Years after Afforestation on Different Parent Material.

The mineralogical composition of the parent material, together with plant species and soil microorganisms, constitutes the foundational components of an ecosystem's energy cycle. Afforestation in arid-semi arid regions plays a crucial role in preventing erosion and enhancing soil quality, offering significant economic and ecological benefits. This study evaluated the effects of afforestation and different parent materials on the physicochemical and microbiological properties of soils, including microbial basal respiration (MR), as well as how these changes in soil properties after 15 years influence plant growth. For this purpose, various soil physicochemical parameters, MR, soil microbial biomass carbon (Cmic), stoichiometry (microbial quotient = Cmic/Corg = qMic and metabolic quotient = MR/Cmic = qCO2), and tree growth metrics such as height and diameter were measured. The results indicated that when the physicochemical and microbiological properties of soils from different bedrock types, along with the average values of tree growth parameters, were analyzed, afforestation areas with limestone bedrock performed better than those with andesite bedrock. Notably, sensitive microbial properties, such as Cmic, MR, and qMic, were positively influenced by afforestation. The highest values of Cmic (323 μg C g-1) and MR (1.3 CO2-C g-1 h-1) were recorded in soils derived from limestone. In contrast, the highest qCO2 was observed in the control plots of soils with andesite parent material (7.14). Considering all the measured soil properties, the samples can be ranked in the following order: limestone sample (LS) > andesite sample (AS) > limestone control (LC) > andesite control (AC). Similarly, considering measured plant growth parameters were ranked as LS > AS. As a result, the higher plant growth capacity and carbon retention of limestone soil indicate that it has high microbial biomass and microbial activity. This study emphasizes the importance of selecting suitable parent material and understanding soil properties to optimize future afforestation efforts on bare lands.

Greenhouse gas emissions during the rice season are reduced by a low soil C:N ratio using different upland-paddy rotation systems

ContextUpland-paddy rotation can improve multiple-cropping index and crop yields; however, the mechanisms underlying the effects of dry-season crop diversification on rice yields and greenhouse gas (GHG) emissions under multiple rotation systems remain unclear. ObjectiveHere, we aimed to clarify the intrinsic mechanisms whereby rice yields and GHG emissions respond to the diversification of dry-season crops and lay a theoretical foundation for developing agronomic measures that can stabilize yields and reduce GHG emissions. MethodsUsing a positioning experimental site for upland-paddy rotation, we measured rice-season CH4 and N2O emissions, crop yields, GHG-emission intensity (GHGI) levels, soil physical and chemical properties in garlic–rice (GR), wheat–rice (WR) systems for 3 years (2019–2020, and 2022), and in a rapeseed–rice (RR) system for 1 year (2022). The soil microbial dynamics of the three systems were only tested in 2022. ResultsThe WR system had the highest CO2 emission equivalent (CO2-eq), with a 3-year interval value of 1898.24–16794.30 kg·ha−1, the lowest yield (8490.10–9773.46 kg·ha−1), and the highest GHGI (0.22–1.83). The GR system had the highest rice yield (9718.91–10769.75 kg ha−1), a lower CO2-eq (1588.55–12567.51 kg·ha−1), and therefore a lower GHGI (0.16–1.24). The RR system had the lowest GHGI in 2022 (benefiting from the lowest CO2-eq) and a slightly higher yield than that of the WR system. CH4 contributed to >88 % of the CO2-eq under the three systems in 2020 and 2022. The higher soil C:N ratio of the WR system stimulated methanogenic microorganisms, coupled with higher microbial biomass C levels, and ultimately increased CH4 emissions substantially. The soil C:N ratios of the GR and RR systems were significantly lower than that of the WR system because the soil total nitrogen (TN) of both systems was higher and increased CH4 emissions were avoided. The higher levels of N nutrients (TN, NO3--N, and NH4+-N) in the GR and RR systems also enhanced rice yields, with respective increases of 10.37 % and 1.22 %, compared with that of the WR system. ConclusionsThe diversified cultivation of dry-season crops in upland-paddy rotation systems affected rice yields and GHG emissions by changing the ratios of C and N. ImplicationsOur findings highlight the importance of future research involving comprehensive agronomic measures to help reduce emissions, including fertilizer management, straw management, and tillage methods.

The spatial distribution of tree-tree interaction effects on soil microbial biomass and respiration.

The capacity of forests to sequester carbon in both above- and belowground compartments is a crucial tool to mitigate rising atmospheric carbon concentrations. Belowground carbon storage in forests is strongly linked to soil microbial communities that are the key drivers of soil heterotrophic respiration, organic matter decomposition and thus nutrient cycling. However, the relationships between tree diversity and soil microbial properties such as biomass and respiration remain unclear with inconsistent findings among studies. It is unknown so far how the spatial configuration and soil depth affect the relationship between tree richness and microbial properties. Here, we studied the spatial distribution of soil microbial properties in the context of a tree diversity experiment by measuring soil microbial biomass and respiration in subtropical forests (BEF-China experiment). We sampled soil cores at two depths at five locations along a spatial transect between the trees in mono- and hetero-specific tree pairs of the native deciduous species Liquidambar formosana and Sapindus saponaria. Our analyses showed decreasing soil microbial biomass and respiration with increasing soil depth and distance from the tree in mono-specific tree pairs. We calculated belowground overyielding of soil microbial biomass and respiration - which is higher microbial biomass or respiration than expected from the monocultures - and analysed the distribution patterns along the transect. We found no general overyielding across all sampling positions and depths. Yet, we encountered a spatial pattern of microbial overyielding with a significant microbial overyielding close to L. formosana trees and microbial underyielding close to S. saponaria trees. We found similar spatial patterns across microbial properties and depths that only differed in the strength of their effects. Our results highlight the importance of small-scale variations of tree-tree interaction effects on soil microbial communities and functions and are calling for better integration of within-plot variability to understand biodiversity-ecosystem functioning relationships.

Optimal enzyme allocation leads to the constrained enzyme hypothesis: the Soil Enzyme Steady Allocation Model (SESAM; v3.1)

Abstract. Describing the coupling of nitrogen (N), phosphorus (P), and carbon (C) cycles of land ecosystems requires understanding microbial element use efficiencies of soil organic matter (SOM) decomposition. These efficiencies are studied by the Soil Enzyme Steady Allocation Model (SESAM) at the decadal scale. The model assumes that the soil microbial communities and their element use efficiencies develop towards an optimum where the growth of the entire community is maximized. Specifically, SESAM approximated this growth optimization by allocating resources to several SOM-degrading enzymes proportional to the revenue of these enzymes, called the Relative approach. However, a rigorous mathematical treatment of this approximation has been lacking so far. Therefore, in this study we derive explicit formulas of enzyme allocation that maximize the total return from enzymatic processing, called the Optimal approach. Further, we derive another heuristic approach that prescribes the change of allocation without the need of deriving a formulation for the optimal allocation, called the Derivative approach. When comparing predictions across these approaches, we found that the Relative approach was a special case of the Optimal approach valid at sufficiently high microbial biomass. However, at low microbial biomass, it overestimated allocation to the enzymes having lower revenues compared to the Optimal approach. The Derivative-based allocation closely tracked the Optimal allocation. These findings increase our confidence in conclusions drawn from SESAM studies. Moreover, the new developments extend the range of conditions at which valid conclusions can be drawn. Further, based on these findings we formulated the constrained enzyme hypothesis. This hypothesis provides a complementary explanation why some substrates in soil are preserved over decades, although they are often decomposed within a few years in incubation experiments. This study shows how optimality considerations lead to simplified models, new insights, and new hypotheses. This is another step in deriving a simple representation of an adaptive microbial community, which is required for coupled stoichiometric C–N–P dynamic models that are aimed to study decadal processes beyond the ecosystem scale.

Evaluation of polyhydroxyalkanoate recovery from food waste by sequencing batch biofilm reactor with high mixed microbial biomass

In this study, the enrichment sequencing batch biofilm reactor (SBBR) and conventional enrichment reactor (SBR) were established, and a new strategy was developed to achieve higher biomass yield and polyhydroxyalkanoate (PHA) production from food waste than those achieved through the conventional method. After the 10th day of an expanded cultivation period, the respective active biomass concentrations in SBR and SBBR were 5.16 and 13.92 g/L, indicating a significant improvement in the biomass yield of mixed microbial culture in the SBBR. The PHA accumulation test revealed that maximum PHA concentration in SBR and SBBR reached 6.60 and 12.70 g/L, respectively, after 80 days of enrichment, indicating that compared to SBR, the SBBR could more effectively improve the PHA accumulation capacity. Meganema, Thauera, and Paracoccus were the dominant PHA-accumulating bacteria in the SBR and SBBR. Additionally, the volumetric productivity of the SBBR was 3.22 g COD/L/d, twice that of the SBR. This study provides new strategies and insights for improving PHA production and reducing the costs of PHA production and reactor investment.

Mineral protection mediates soil carbon temperature sensitivity of nine old-growth temperate forests across the latitude transect

Temperature sensitivity (Q10) of soil microbial respiration serves as a crucial indicator for assessing the response of soil organic carbon (SOC) to global warming. However, the biogeographic variation in Q10 remains inconsistent. In this study, we examined Q10 and its potential drivers in nine old-growth mixed broad-leaved Korean pine (Pinus koraiensis Sieb. et Zucc.) forests (the climax community of Asian temperate mixed forest) under a wide range of climatic conditions. We found that stand characteristics (arbuscular mycorrhizal tree basal area to ectomycorrhizal tree basal area ratio and root to shoot ratio) contributed to soil C sequestration by facilitating the accumulation of soil recalcitrant C components. Contrary to the C quality-temperature hypothesis, Q10 was not correlated with C quality (soil C to nitrogen ratio and recalcitrant C to labile C ratio). Soil mineral protection parameters (Fe/Al oxides) had negative effect on Q10 because they inhibited microbial activities by decreasing substrate accessibility. Additionally, soils with high microbial biomass C and microbial biomass C to soil organic C ratio had high Q10. Overall, understanding the complex relationships among Q10, mineral protection, and microbial attributes on a spatial scale is essential for accurately predicting soil C cycling in forest ecosystems.

Nitrogen Application Timing and Levels Affect the Fate and Budget of Fertilizer Nitrogen in the Apple-Soil System.

This study aimed to determine the effects of the nitrogen (N) application period and level on the fate of fertilizer N and the contribution of N absorption and translocation to apple organ N. Two N application periods (labeled by the 15N tracer technique in spring and summer, represented by SP and SU, respectively) and three N levels (N0, MN, and HN) were used to determine the physiological indexes and aboveground, root, and soil 15N content of 4-year-old dwarf ('Red Fuji'/M9T337) and arborized ('Red Fuji'/Malus hupehensis Rehd.) apple trees. The results showed that HN led to shoot overgrowth, which was not conducive to the growth of the apple root system (root length, root tips, root surface area, and root volume) or the improvement of root activity. The contribution of soil N to apple organ N accounted for more than 50%, and the contribution of N application in summer to fruit N was higher than that in spring. Under HN treatment, the proportion of soil N absorbed by trees decreased, while that of fertilizer N increased; however, the highest proportion was still less than 50%, so apple trees were highly dependent on soil N. Under MN treatment, fertilizer N residue was similar to soil N consumption, and soil N fertility maintained a basic balance. Under HN treatment, fertilizer N residue was significantly higher than soil N consumption, indicating that excessive N application increased fertilizer N residue in the soil. Overall, the 15N utilization rate of arborized trees (17.33-22.38%) was higher than that of dwarf trees (12.89-16.91%). A total of 12.89-22.38% of fertilizer 15N was absorbed by trees, 30.37-35.41% of fertilizer 15N remained in the soil, and 44.65-54.46% of fertilizer 15N was lost. The 15N utilization rate and 15N residual rate of summer N application were higher than those of spring N application, and the 15N loss rate was lower than that of spring N application. High microbial biomass N (MBN) may be one of the reasons for the high N utilization rate and the low loss rate of N application in summer.

Toward soil carbon storage: The influence of parent material and vegetation on profile-scale microbial community structure and necromass accumulation

Soil microbial communities play a crucial role in the accumulation and stabilization of soil organic carbon (SOC) through complex processes involving plant residue transformation and mineral interactions. These processes are influenced by plant inputs and modulated by soil properties that are mostly determined by the parent material. However, our understanding is limited regarding the manner in which vegetation and parent material affect microbial community structure, necromass accumulation, and their subsequent impact on SOC storage. To bridge this knowledge gap, we conducted an in-depth investigation focusing on the top-down influence of vegetation type and the bottom-up effect of parent material on microbial-mediated carbon transformation across soil profiles in a tropical region. Our study encompassed 42 sites on three parent materials (basalt, granite, and marine sediments) and four vegetation types (rubber, banana, areca plantations and uncultivated grassland). Soil samples were collected at 0–20, 20–40, 40–80, and 80–100 cm depth. Microbial community structure and necromass were quantified using microbial biomarkers of phospholipid fatty acids and amino sugars, respectively. In rubber plantations, we observed a trend toward higher microbial biomass that, though not significant when compared to other vegetation types, transformed to a significantly higher accumulation of microbial necromass. This increase in microbial necromass was linked to the accumulation of SOC facilitated by the presence of clay size minerals in clayey soils developed from basalt. In particular, basaltic soils were dominated by bacteria, which facilitated the accumulation of bacterial necromass that significantly bolstered its contribution to SOC. In contrast, in sandier soils developed from granite and marine sediments, fungal communities and necromass dominated due to the propensity of fungi for coarser soil environments. Overall, the main impact of vegetation on microbial communities and necromass accumulation was primarily demonstrated for the topsoil. Differences in soil texture arising from different parent materials exert significant effects on the fungal-to bacterial-biomass and necromass ratios, consequently influencing the contribution of fungal and bacterial necromass carbon to SOC across soil profiles. Our study underscores the pivotal role of parent material in governing tropical profile-scale soil carbon storage by shaping the structure of microbial communities and influencing the retention of microbial necromass.

Fungal community composition changes and reduced bacterial diversity drive improvements in the soil quality index during arable land restoration

Arable land is facing the growing challenge of land degradation due to intensive use and this is beginning to affect global food security. However, active and passive restoration can improve soil characteristics and reshape microbial communities. Despite the increasing focus on changes in microbial communities during restoration, the mechanisms underlying how microbes drive the soil quality index (SQI) in arable land restoration remain unclear. In this study, we selected conventional farmland (CF, heavily intensified) and two restoration strategies (AR, artificial restoration; NR, natural restoration), with the same context (including soil texture, climate, etc.), and measured the microbial indicators over 2 years to investigate the mechanisms driving SQI improvement on restored arable land. The AR and NR treatments resulted in a 50% and 58% increase in SQI, respectively, compared to CF as soil nutrient levels increased, resulting in higher microbial biomasses and enzyme activities. Microbial abundance on the AR land was approximately two times greater than on the NR land due to the introduction of legumes. Bacterial diversity declined, while fungi developed in a more diverse direction under the restoration strategies. The AR and NR areas were mainly enriched with rhizobium (Microvirga, Bradyrhizobium), which contribute to healthy plant growth. The pathogenic fungi (Gibberella, Fusarium, Volutella) were more abundant in the CF area and the plant pathogen guild was about five times higher in the restored areas. Following arable land restoration, microbial life history strategies shifted from r-to K-strategists due to the higher proportion of recalcitrant SOC (DOC/SOC decreased by 18%–30%). The altered microbial community in the restored areas created new levels of functionality, with a 2.6%–4.3% decrease in bacterial energy metabolism (oxidative phosphorylation, C fixation, and N metabolism decreased by 7%, 4%, and 6%, respectively). Structural equation modelling suggested that restoration strategy affected SQI either directly by increasing total soil nutrient levels or indirectly by altering the microbial community and that fungal community composition and bacterial diversity made the largest contributions to SQI. These results provided new insights into soil quality improvement from a microbial perspective and can help guide future arable land restoration.

Effect of vermicompost on soil quality parameters for different land use patterns

Extensive industrialization, urbanization, and excessive use of chemicals in agricultural practices have caused soil quality depletion and reduced its nutritional value. In this context, the present study aimed to evaluate the effect of vermicompost (VC) on different soil properties such as pH, electrical conductivity, soil organic carbon, soil organic matter, total phosphorus, and bulk density to understand the soil enrichment for different land use patterns i.e., agriculture soil (AS), forest soil (FS) and barren soil (BS). The collected soil samples were mixed with VC in different proportions (1:1, 1:2, 1:3, 1:4, and 1:5) and analyzed in terms of aforementioned parameters. Among the investigated soils, the highest microbial biomass was observed for FS samples and noted in the range of 6 – 8 mg/gm of soil. All the original soils, supplemented samples, and VC were also subjected to plant growth analysis. The soil quality index (SQI) was determined using principal component analysis for selected soil samples and resulted mixtures obtained from soil and various proportions of VC. Among all samples, highest SQI was observed as 0.785 for VC. Overall, the result of the study showed that vermicompost can be a potential substitute of chemical fertilizers, thus improving the soil quality and crop yield.

Microbial gene abundance mirrors soil nitrogen mineralization intensity across an age gradient in Chinese-fir plantations

Stand development affects soil properties, nitrogen (N) dynamics, and soil microbial community composition, but the question remains whether differences in N mineralization rates are mirrored by the abundance of relevant functional genes. In this study, we used the 15N pool-dilution method to estimate N mineralization (i.e., ammonification and nitrification) rates across a Chinese fir (Cunninghamia lanceolata) chronosequence, with stands aged 7, 16, 29, 36, and >80 years. Gene copy numbers of bacteria (16S rRNA), fungi (ITS), ammonia-oxidizing archaea (AOA) and bacteria (AOB) (amoA), denitrifiers (nirS, nirK), N2 fixers (nifH) and organic N decomposers (chiA) were quantified by qPCR. Gross ammonification and nitrification rates increased linearly with stand age in the topsoil (0–5 cm depth) and were strongly positively correlated with the abundance of the bacterial 16S rRNA gene and AOA amoA, respectively. Higher net nitrification but lower NO3− immobilization rates in older stands (32 and > 80 years) drove higher N availability for vegetation than in young stands (7 years). Older stands also had higher rates of NH4+ consumption than younger stands due to the increased fungal ITS abundance and higher microbial biomass N (MBN), and AOA amoA was more abundant and active than AOB amoA due to the more acid conditions characteristic of mature forests. Redundancy analysis showed that functional gene abundance was strongly affected by soil properties such as pH, NH4+-N content, and MBN. We also found that microbial N storage potential was lower, and the NO3−-N leaching and gaseous N loss potential were higher in older stands than in younger stands. Collectively, stand developmental stage gave rise to the observed spatial gradient of gross ammonification and nitrification rates by altering the abundance of microbial functional genes, which affected plantation productivity via its modulation of the supply of bioavailable N.

Seasonal Relationships of Alpine Plants and Microbes through a Stoichiometric and Enzymatic Lens

Alpine biomes experience harsh environmental conditions and short growing seasons, which necessitate interspecific and intraspecific interactions to ensure the stability of diversity and ecosystem multifunctionality. The relationship between plants and microbes in this environment is equally dynamic, with seasonal pulses of nutrients and the phenology of plants creating specific "hot moments" of biogeochemical activity. As a crucial zone of interaction between plant roots and microbial communities, the rhizosphere serves as a "hot spot" of biogeochemical cycling where the mineralization of nutrients, such as carbon, nitrogen, and phosphorus, allows for the transfer of nutrients between trophic levels. However, the nature of these interactions depends on edaphic and climatic conditions, potentially leading to cooperation or competition to meet the stoichiometric demands of organisms. Elevation gradients within alpine ecosystems provide dramatic shifts in temperature, precipitation, and soil development that allow for the study of these interactions over short geographical distances. In conjunction with seasonal sampling, this approach can provide a wide environmental context to observe the relationship between specific plants and microbial communities. By investigating the C/N ratios of plants, microbes, and soil, as well as microbial enzymatic potential, we can infer nutrient limitations, temporal niche partitioning, and biological responses to abiotic conditions. Within the Austrian Alps, we studied a selection of herbaceous plants and their associated microbial communities across an elevation gradient spanning 2200-2800 m (Fig. 1). The primary aims of the study were to assess the seasonal changes in C/N stoichiometry from both trophic levels, microbial enzymatic potential, and rhizosphere diversity of bacterial and fungal communities. To fulfill these aims, four locations were selected based on the two present biomes (alpine meadow and sub-nival zone) and the transition between them. Four to five plant species were collected during each season in 2023, including the often-neglected snow-covered winter season, along with rhizosphere and bulk soil for microbial biomass measurements and soil chemistry. Plant leaf tissue samples were analyzed using Isotope-ratio mass spectrometry for plant C/N ratios, while soil and microbial C/N ratios were calculated using chloroform fumigation extraction. Microbial enzymatic potential was assessed using hydrolase enzymatic assays for five fluorophore-labeled substrates. 16S-rRNA and 18S-rRNA genes were sequenced using an Illumina MiSeq platform from the fine roots of collected plant individuals to quantify the relative abundances of bacterial and fungal taxa. The findings of our study indicate that the higher microbial biomass (Cmic) in alpine meadow locations leads to increased enzymatic activity compared to sub-nival zones. However, specific plant species were found to enhance microbial biomass and enzymatic potential in different seasons, suggesting that plants promote microbial interaction and biogeochemical cycling during different seasons as a form of temporal niche partitioning. Most plant species demonstrated an increase in C/N ratios throughout the season, sometimes increasing by more than 200%. However, two Poa spp. showed the highest C/N ratios during the summer, which further correlated with higher microbial C/N ratios. By observing changes in stoichiometric ratios of organisms that interact and share nutrients, we propose that these relationships vary between host plants depending on their temporal niche and abiotic factors (soil and environmental conditions). Furthermore, the positive or negative correlation of plant and microbial C/N ratios may indicate the relative cooperation or competition between trophic levels.

Gross nitrogen transformation rates in shifting cultivation systems in northern Thailand: Controlling factors and implications for inorganic nitrogen availability

Slash-and-burn practices and subsequent fallow periods affect soil nitrogen (N) availability. Although extensive studies have examined the global temporal patterns of inorganic N after fire, NO3− regulation remains unclear due to ecosystem-dependent responses. Despite inorganic N pool control by NH4+ and NO3− production and consumption, local-scale patterns and mechanisms of gross N transformations, particularly in tropical regions, remain insufficiently understood. Thus, we aimed to elucidate the controlling factors of inorganic N in the shifting cultivation cycle in Northern Thailand, using a 15N pool dilution method on soil samples at 0–10 cm depth collected across various post-burning stages (1, 4, 6, and 7 years after burning) and forest. We found that gross ammonification was enhanced by high soil organic matter and microbial biomass, while gross nitrification was enhanced by greater soil alkalinity. Ammonium immobilization increased with higher microbial biomass, while NO3− immobilization increased with lower NH4+ availability. With increasing fallow period, microbial biomass and consequently gross ammonification increased, boosting the NH4+ pool. Soil acidity, correlated with soil texture, influenced nitrification: coarser-textured soil intensified acidity and decreased gross nitrification, resulting in NH4+-dominance, while finer-textured soil alleviated acidity, promoting nitrification over NH4+ immobilization, leading to NO3−-dominance. Our findings confirm that the fallow stage, along with which microbial biomass increases, was an essential driving factor regulating ammonification, while soil acidity, unrelated to fallow but a function of sand/silt content, was an essential driving factor regulating nitrification under shifting cultivation in Northern Thailand.

Interactive effect of biochar and urea addition increases plant growth and rhizosphere microbial activity and decreases N2O emissions

Simultaneous addition of biochar with applied N fertilizer was proposed as useful way how to improve soil fertility and reduce negative effects of nitrogen fertilization. A hypothesis that added N decreases root growth and soil microbial activity and increases N2O emissions while addition of biochar has opposite effect was tested. We further hypothesized that increased microbial activity in biochar-amended soil stimulates growth of subsequently cultivated plants.The supposed interactive effect of biochar and N-fertilizer was studied in pot experiment with cultivation of lettuce in soil amended with urea, biochar and their combination. In each pot, yield of plant biomass was determined and basal respiration, substrate-induced respiration and content of mineral N were determined in soil samples. Soil with roots decomposing after lettuce harvest was also analyzed and subsequently used for the cultivation of wheat plants.Emissions of N2O were measured following N application and measurement continued after harvest. Contrary to the hypothesis, N fertilization stimulated the growth of not only aboveground but also belowground plant biomass. Biochar increased growth of roots in agreement with the hypothesis. The effect of treatments on microbial biomass and respiration was relatively weak in the rhizosphere of growing plants. However, when roots were decomposed, lower Nmin and higher microbial biomass were observed in biochar amended soils. Biochar amendment significantly stimulated the yield of subsequently cultivated wheat. At the beginning of the experiment, N2O emissions were higher in biochar-amended soil. However, at the later phase of the experiment, cumulative emissions were lower in biochar-amended soils. Results suggest that biochar supports more efficient N utilization by plants and increases soil fertility. Biochar also decreases N losses through N2O emissions, even with simultaneous N fertilization.

Microbial responses to soil cooling might explain increases in microbial biomass in winter

In temperate, boreal and arctic soil systems, microbial biomass often increases during winter and decreases again in spring. This build-up and release of microbial carbon could potentially lead to a stabilization of soil carbon during winter times. Whether this increase is caused by changes in microbial physiology, in community composition, or by changed substrate allocation within microbes or communities is unclear. In a laboratory incubation study, we looked into microbial respiration and growth, as well as microbial glucose uptake and carbon resource partitioning in response to cooling. Soils taken from a temperate beech forest and temperate cropland system in October 2020, were cooled down from field temperature of 11 °C to 1 °C. We determined microbial growth using 18O-incorporation into DNA after the first two days of cooling and after an acclimation phase of 9 days; in addition, we traced 13C-labelled glucose into microbial biomass, CO2 respired from the soil, and into microbial phospholipid fatty acids (PLFAs). Our results show that the studied soil microbial communities responded strongly to soil cooling. The 18O data showed that growth and cell division were reduced when soils were cooled from 11 to 1 °C. Total respiration was also reduced but glucose uptake and glucose-derived respiration were unchanged. We found that microbes increased the investment of glucose-derived carbon in unsaturated phospholipid fatty acids at colder temperatures. Since unsaturated fatty acids retain fluidity at lower temperatures compared to saturated fatty acids, this could be interpreted as a precaution to reduced temperatures. Together with the maintained glucose uptake and reduced cell division, our findings show an immediate response of soil microorganisms to soil cooling, potentially to prepare for freezing events. The discrepancy between C uptake and cell division could explain previously observed high microbial biomass carbon in temperate soils in winter.

Close coupling of plant functional types with soil microbial community composition drives soil carbon and nutrient cycling in tundra heath

AimsThis study aimed at elucidating divergent effects of two dominant plant functional types (PFTs) in tundra heath, dwarf shrubs and mosses, on soil microbial processes and soil carbon (C) and nutrient availability, and thereby to enhance our understanding of the complex interactions between PFTs, soil microbes and soil functioning.MethodsSamples of organic soil were collected under three dwarf shrub species (of distinct mycorrhizal association and life form) and three moss species in early and late growing season. We analysed soil C and nutrient pools, extracellular enzyme activities and phospholipid fatty acid profiles, together with a range of plant traits, soil and abiotic site characteristics.ResultsShrub soils were characterised by high microbial biomass C and phosphorus and phosphatase activity, which was linked with a fungal-dominated microbial community, while moss soils were characterised by high soil nitrogen availability, peptidase and peroxidase activity associated with a bacterial-dominated microbial community. The variation in soil microbial community structure was explained by mycorrhizal association, root morphology, litter and soil organic matter quality and soil pH-value. Furthermore, we found that the seasonal variation in microbial biomass and enzyme activities over the growing season, likely driven by plant belowground C allocation, was most pronounced under the tallest shrub Betula nana.ConclusionOur study demonstrates a close coupling of PFTs with soil microbial communities, microbial decomposition processes and soil nutrient availability in tundra heath, which suggests potential strong impacts of global change-induced shifts in plant community composition on carbon and nutrient cycling in high-latitude ecosystems.

The Effect of Plant Diversity and Soil Properties on Soil Microbial Biomass and Activity in a Novel Ecosystem

Plant–microbial relations have not yet been fully disclosed in natural or seminatural ecosystems, nor in novel ecosystems developing spontaneously on post-coal mine heaps. The aim of this study was to determine which factor, biotic (plant taxonomic diversity vs. plant functional diversity) or abiotic (physicochemical substrate parameters), affects the biomass of soil microbial communities the most, as well as soil in situ respiration in novel ecosystems. The study was carried out on unreclaimed plots selected according to four different combinations of taxonomic and functional plant diversity. Additionally, plots on a reclaimed heap served as a comparison between the two management types. The biomass of several soil microbial groups was analysed using phospholipid fatty acids profiles. We detected that soil microbial biomass was more impacted by abiotic parameters (explaining 23% of variance) than plant diversity (explaining 12% of variance). Particularly, we observed that substrate pH was the most important factor shaping microbial community biomass, as shown in the RDA analysis. The highest microbial biomass was found in plots with low taxonomic and functional diversity. This finding can be explained by the fact that these plots represented a more advanced phase of vegetation development in the early stages of plant succession.