Microbial Biomass Community Research Articles

Drivers of microbial carbon biomass variability in two oceanic regions of the Gulf of Mexico

The microbial plankton community is an integral part of the pelagic ecosystem. It hosts essential functional groups that play a vital role in organic carbon production, release, uptake, and degradation within open-ocean ecosystems. Given its significance, carbon biomass estimates are urgently needed, especially in oligotrophic regions, to provide and enhance our knowledge of biogenic carbon pools. They also aid in validating biogeochemical models that characterize the functioning of these extensive marine ecosystems within the global carbon cycle. This study addresses the temporal variability of microbial community biomass in two oceanic zones: the west-central (Perdido) and southern (Coatzacoalcos) areas of the Gulf of Mexico. During three seasonally contrasting periods (nortes, rainy, and dry seasons), seawater samples were collected from the euphotic zone in both regions to estimate the carbon biomass of different pico- (<2–3 µm), nano-, and microplankton groups (>3–200 µm). Carbon biomass assessments for the microbial groups were based on their abundance and carbon conversion factors. Overall, we found a significant contribution of pico-prokaryotic components (heterotrophic bacteria, Prochloroccocus, and Synechoccocus) to the total microbial carbon stock of the euphotic zone (84–89 % global estimates). The finding suggests these microorganisms are key functional groups that drive carbon production and fate in the Gulf of Mexico ecosystem. Pico-cyanobacteria, especially Prochloroccocus, were the dominant primary producers (68–82 % total autotrophic carbon), mainly in the upper layer of the oligotrophic euphotic zone. This vertical pattern implies that the deep chlorophyll-a maximum (DCM) depth level was unrelated to a net increase in phytoplankton biomass in the three study periods. The distribution of microbial carbon biomass exhibited striking differences associated with winter mixing (the nortes season), high river discharge accompanied by cross-shelf transport (the rainy season), and the dynamics of mesoscale structures. Ecological aspects, such as the habitat preference of the organisms and the seasonal complementary development of mixotrophic and heterotrophic grazers and their prey, were also essential drivers in regulating the microbial carbon pool of both oceanic regions. The microbial carbon assessments conducted in this study contribute to identifying and quantifying key planktonic functional groups involved in the biogeochemical carbon cycle in the Gulf of Mexico open-ocean ecosystem.

Biomass and Functional Diversity of Microbial Communities in Catenas of Virgin and Arable Gray Soils and Chernozems

Biomass and Functional Diversity of Microbial Communities in Catenas of Virgin and Arable Gray Soils and Chernozems

Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities.

Microbial inoculation involves transplanting microorganisms from their natural habitat to new plants or soils to improve plant performance, and it is being increasingly used in agriculture and ecological restoration. However, microbial inoculants can invade and alter the composition of native microbial communities; thus, a comprehensive analysis is urgently needed to understand the overall impact of microbial inoculants on the biomass, diversity, structure and network complexity of native communities. Here we provide a meta-analysis of 335 studies revealing a positive effect of microbial inoculants on soil microbial biomass. This positive effect was weakened by environmental stress and enhanced by the use of fertilizers and native inoculants. Although microbial inoculants did not alter microbial diversity, they induced major changes in the structure and bacterial composition of soil microbial communities, reducing the complexity of bacterial networks and increasing network stability. Finally, higher initial levels of soil nutrients amplified the positive impact of microbial inoculants on fungal biomass, actinobacterial biomass, microbial biomass carbon and microbial biomass nitrogen. Together, our results highlight the positive effects of microbial inoculants on soil microbial biomass, emphasizing the benefits of native inoculants and the important regulatory roles of soil nutrient levels and environmental stress.

Parental material and climate jointly determine the biomass and diversity of soil microbial communities along an elevational gradient on a subtropical karst mountain

AbstractAimClimate is widely understood to determine elevational patterns of soil microbial communities, whereas the effects of parental material are uncertain. Changes in the composition of parental materials along elevational transects could also affect soil microbial communities by influencing soil pH and nutrient availability. Here, we aim to illustrate the combined effects of climate and parental material on the biomass and composition of soil microbial communities along an elevational transect.LocationA subtropical forest on a karst mountain (Mt. Jinfo), China.TaxonBacteria and Fungi.MethodsWe use phospholipid fatty acid analysis (PLFA) and DNA amplicon high‐throughput sequencing to determine biomass and diversity patterns of soil microbial communities along a subtropical elevational gradient with contrasting parental materials (limestone and clasolite).ResultsWe observed that the microbial communities were more diverse (α‐diversity) and productive (biomass) on limestone than on clasolite. Additionally, we found that parental material played a role in shaping the composition (β‐diversity) of soil microbial communities along the elevational gradient. The impact of climate on soil microbial communities was found to be significant, albeit relatively weak. Structural equation models provided evidence for both direct and indirect effects of climate and parental material on microbial biomass and α‐diversity along the elevational gradient. Notably, the changes in soil pH, influenced by both parental material and climate, were identified as a key factor driving these effects.Main ConclusionsOur results underline the importance of both climate and parental material variations in space‐for‐time studies investigating soil microbial communities along elevational gradients.

Biomass and Functional Diversity of Microbial Communities in Catenas of Reserved and Arable Gray Soils and Chernozems

Biomass and Functional Diversity of Microbial Communities in Catenas of Reserved and Arable Gray Soils and Chernozems

Quality matters: Response of bacteria and ciliates to different allochthonous dissolved organic matter sources as a pulsed disturbance in shallow lakes

Shallow lake ecosystems are particularly prone to disturbances such as pulsed dissolved organic matter (allochthonous-DOM; hereafter allo-DOM) loadings from catchments. However, the effects of allo-DOM with contrasting quality (in addition to quantity) on the planktonic communities of microbial loop are poorly understood. To determine the impact of different qualities of pulsed allo-DOM disturbance on the coupling between bacteria and ciliates, we conducted a mesocosm experiment with two different allo-DOM sources added to mesocosms in a single-pulse disturbance event: Alder tree leaf extract, a more labile (L) source and HuminFeed® (HF), a more recalcitrant source. Allo-DOM sources were used as separate treatments and in combination (HFL) relative to the control without allo-DOM additions (C). Our results indicate that the quality of allo-DOM was a major regulator of planktonic microbial community biomass and/or composition through which both bottom-up and top-down forces were involved. Bacteria biomass showed significant nonlinear responses in L and HFL with initial increases followed by decreases to pre-pulse conditions. Ciliate biomass was significantly higher in L compared to all other treatments. In terms of composition, bacterivore ciliate abundance was significantly higher in both L and HFL treatments, mainly driven by the bacterial biomass increase in the same treatments. GAMM models showed negative interaction between metazoan zooplankton biomass and ciliates, but only in the L treatment, indicating top-down control on ciliates. Ecosystem stability analyses revealed overperformance, high resilience and full recovery of bacteria in the HFL and L treatments, while ciliates showed significant shift in compositional stability in HFL and L with incomplete taxonomic recovery. Our study highlights the importance of allo-DOM quality shaping the response within the microbial loop not only through triggering different scenarios in biomass, but also the community composition, stability, and species interactions (top-down and bottom-up) in bacteria and plankton.

Short-Term PE Generation Processes in the Soils of a Farmer Plots Network in the Madagascar Highlands: Actors and Drivers

Carbon sequestration in agricultural soils, through the accumulation of high-quality organic matter, represents great potential to mitigate climate change and simultaneously improve soil fertility. Such a challenge is particularly important and relevant in developing tropical countries like Madagascar, where soil carbon storage is vulnerable to climatic variations and where fertilization is generally applied through amendments in organic matter of various origins. The priming effect (PE) is considered here as the stimulation of the mineralization of soil organic matter (SOM) by a supply of fresh organic matter (FOM). PE results from different microbial processes driven by specific biotic and abiotic parameters. Depending on the processes involved, it has been suggested that PE could either counteract SOM accumulation or promote it. The objective of the present study was to explore the relationships between certain agricultural practices (type of crop, quality of fertilization, association with trees), the potential intensity of PE, as well as several abiotic (texture, quantity and quality SOM, nutrient enrichment) a1nd biotic (biomass and phylogenetic composition of microbial communities) factors which have been proposed in the literature as specific determinants of the different PE generation mechanisms. The soils for this study come from a network of farms in a commune in the Highlands of Madagascar. The PE, generated by a supply of 13C-enriched wheat straw, could not directly correlate with agricultural treatments. However, several indirect correlations could be found via several specific abiotic and microbial determinants that are discussed in terms of soil fertility restoration.

Coexisting picoplankton experience different relative grazing pressures across an ocean productivity gradient.

Picophytoplankton populations [Prochlorococcus, Synechococcus (SYN), and picoeukaryotes] are dominant primary producers in the open ocean and projected to become more important with climate change. Their fates can vary, however, with microbial food web complexities. In the California Current Ecosystem, picophytoplankton biomass and abundance peak in waters of intermediate productivity and decrease at higher production. Using experimental data from eight cruises crossing the pronounced CCE trophic gradient, we tested the hypothesis that these declines are driven by intensified grazing on heterotrophic bacteria (HBAC) passed to similarly sized picophytoplankton via shared predators. Results confirm previously observed distributions as well as significant increases in bacterial abundance, cell growth, and grazing mortality with primary production. Mortalities of picophytoplankton, however, diverge from the bacterial mortality trend such that relative grazing rates on SYN compared to HBAC decline by 12-fold between low and high productivity waters. The large shifts in mortality rate ratios for coexisting populations are not explained by size variability but rather suggest high selectivity of grazer assemblages or tightly coupled tradeoffs in microbial growth advantages and grazing vulnerabilities. These findings challenge the long-held view that protistan grazing mainly determines overall biomass of microbial communities while viruses uniquely regulate diversity by "killing the winners".

Microbial Architects of the Cold Deserts: A Comprehensive Research of Biological Soil Crusts in the High-Altitudinal Cold Deserts of the Western Himalayas

Our research has focused on Biological Soil Crusts (BSCs) in the Western Himalayas, specifically in Tibetan Plateau and Karakoram (Ladakh, India) along the elevation gradient spanning a range of 4300–6000 m a.s.l. where habitats like cold deserts, steppes, alpine and subnival vegetation, as well as primary successional stages behind retreating glaciers are present. These regions are characterised by extensive development of BSCs, with cyanobacteria as the dominant component. BSCs are of great significance for the sustainability and development of ecosystems of arid regions worldwide. Their activity is limited to brief periods when precipitation or dew hydrates microbial cells, enabling metabolic activity. Despite the crucial role played by these phototrophic microbial communities in arid and semi-arid ecosystems worldwide, remote mountain regions like the Tibetian Tibetan Plateau and Karakoram have received limited attention in this regard. More than 15 years long research allowed us to determine several critical aspects of BSCs’ activity and performance: We conducted laboratory and in-situ experiments Fig. 1 to assess the potential photosynthetic and heterotrophic activity of BSCs from high-altitude cold deserts. The experiments involved measuring the production and consumption of CO2 and O2 by BSCs under various temperature and moisture conditions, as well as light intensity. By manipulating these factors, we could differentiate the activities of heterotrophs and autotrophs within the BSCs. The results of these experiments were then analysed in the context of soil nutrient stoichiometry, phylogenetic structure, and microbial community biomass. Using these data, we developed a mechanistic mathematical model to predict the overall metabolic activity of BSCs in response to the major climatic drivers: temperature and moisture. This knowledge could help us to predict the reaction of BSC to climatic changes and reveal if the arid areas in Western Himalayas will act as CO2 sources or sink. We further investigated the composition and content of pigments in microbial soil communities across various habitats along the elevation gradient in the Tibetan Plateau (Rehakova and Capkova 2019). Soil microbes have evolved complex metabolic strategies, such as producing photoprotective and photosynthetic pigments, to survive the environmental stress caused by high UV radiation, fluctuating temperatures, and drought. We also examined the effects of environmental factors such as altitude, mountain range, and soil physico-chemical parameters on the composition and biovolume of phototrophs which dominate the BSc in the studied region (Řeháková 2011, Janatková and Řeháková 2013). This was accomplished through multivariate redundancy analysis and variance partitioning. Interestingly, the phylogenetic diversity and morphotypes’ composition were similar between the Karakoram and Tibetan Plateau (Čapková 2015). Our investigation represents the first recorded assessment of the phylogenetic diversity of cyanobacterial communities within biological soil crusts in the Western Himalayas, specifically at altitudes exceeding 5000 m. We conducted laboratory and in-situ experiments Fig. 1 to assess the potential photosynthetic and heterotrophic activity of BSCs from high-altitude cold deserts. The experiments involved measuring the production and consumption of CO2 and O2 by BSCs under various temperature and moisture conditions, as well as light intensity. By manipulating these factors, we could differentiate the activities of heterotrophs and autotrophs within the BSCs. The results of these experiments were then analysed in the context of soil nutrient stoichiometry, phylogenetic structure, and microbial community biomass. Using these data, we developed a mechanistic mathematical model to predict the overall metabolic activity of BSCs in response to the major climatic drivers: temperature and moisture. This knowledge could help us to predict the reaction of BSC to climatic changes and reveal if the arid areas in Western Himalayas will act as CO2 sources or sink. We further investigated the composition and content of pigments in microbial soil communities across various habitats along the elevation gradient in the Tibetan Plateau (Rehakova and Capkova 2019). Soil microbes have evolved complex metabolic strategies, such as producing photoprotective and photosynthetic pigments, to survive the environmental stress caused by high UV radiation, fluctuating temperatures, and drought. We also examined the effects of environmental factors such as altitude, mountain range, and soil physico-chemical parameters on the composition and biovolume of phototrophs which dominate the BSc in the studied region (Řeháková 2011, Janatková and Řeháková 2013). This was accomplished through multivariate redundancy analysis and variance partitioning. Interestingly, the phylogenetic diversity and morphotypes’ composition were similar between the Karakoram and Tibetan Plateau (Čapková 2015). Our investigation represents the first recorded assessment of the phylogenetic diversity of cyanobacterial communities within biological soil crusts in the Western Himalayas, specifically at altitudes exceeding 5000 m.

Soil microbial community parameters affected by microplastics and other plastic residues.

The impact of plastics on terrestrial ecosystems is receiving increasing attention. Although of great importance to soil biogeochemical processes, how plastics influence soil microbes have yet to be systematically studied. The primary objectives of this study are to evaluate whether plastics lead to divergent responses of soil microbial community parameters, and explore the potential driving factors. We performed a meta-analysis of 710 paired observations from 48 published articles to quantify the impact of plastic on the diversity, biomass, and functionality of soil microbial communities. This study indicated that plastics accelerated soil organic carbon loss (effect size = -0.05, p = 0.004) and increased microbial functionality (effect size = 0.04, p = 0.003), but also reduced microbial biomass (effect size = -0.07, p < 0.001) and the stability of co-occurrence networks. Polyethylene significantly reduced microbial richness (effect size = -0.07, p < 0.001) while polypropylene significantly increased it (effect size = 0.17, p < 0.001). Degradable plastics always had an insignificant effect on the microbial community. The effect of the plastic amount on microbial functionality followed the "hormetic dose-response" model, the infection point was about 40 g/kg. Approximately 3564.78 μm was the size of the plastic at which the response of microbial functionality changed from positive to negative. Changes in soil pH, soil organic carbon, and total nitrogen were significantly positively correlated with soil microbial functionality, biomass, and richness (R2 = 0.04-0.73, p < 0.05). The changes in microbial diversity were decoupled from microbial community structure and functionality. We emphasize the negative impacts of plastics on soil microbial communities such as microbial abundance, essential to reducing the risk of ecological surprise in terrestrial ecosystems. Our comprehensive assessment of plastics on soil microbial community parameters deepens the understanding of environmental impacts and ecological risks from this emerging pollution.

Soil Microbial Community and Soil Abiotic Factors Are Linked to Microorganisms’ C:N:P Stoichiometry in Larix Plantations

Ecological stoichiometry is an essential tool to understand carbon (C), nitrogen (N), and phosphorus (P) cycles and nutrient limitations. Plantations are usually managed to maintain specific age structures, but the impact of such management on microbial biomass and stoichiometric ratios remains unclear. We compared the stand ages of four Larix principis-rupprechtti Mayr. Plantations that were 15 years old, (young plantation, Lar15), 24 years old, (middle aged plantation, Lar24), 40 years old, (near-mature plantation, Lar40), and 50 years old, (mature plantation, Lar50), respectively, to determine the main factors that drive differences in the C:N:P stoichiometry of microorganisms. We demonstrated that the temperature, moisture, and nutrient concentrations in surface soil increased significantly with forest age. The stoichiometric ratios of elements in soil and microorganisms reached their maxima in the Lar40 and Lar50 plantations. Additionally, forest stand ages had a great influence on the biomass of microbial communities. Moreover, soil microbial community and soil abiotic factors are closely related to soil microorganisms’ C:N:P stoichiometric ratios. Specifically, changes in the microbial biomass C:N (MBC:MBN) were primarily correlated with bacteria, Gram-positive bacteria (G+), temperature, NH4+-N, and moisture in soil. Shifts in G+, actinobacteria, soil temperature, and total phosphorus were primarily associated with variation in microbial biomass C:P (MBC:MBP). Alterations in microbial biomass N:P (MBN:MBP) were correlated with bacteria, NH4+-N, water content, Gram-negative bacteria, and soil temperature. Overall, these results suggest that microbial elemental stoichiometric ratios could be affected by stand age and emphasize the importance of microbial communities and soil abiotic factors in shifting this dynamic change process.

Summer heatwaves affect coastal Antarctic plankton metabolism and community structure

In the austral summer of 2020, record high temperatures were registered in the Western Antarctic Peninsula. This offered a unique opportunity to evaluate the effect of extreme sea surface temperature and natural heatwaves on the metabolic balance (i.e. the balance between production and respiration), lipid damage and the possible change in lipid composition of coastal Antarctic (Potter Cove, King George/25 de Mayo Island, South Shetlands) microbial communities. Two marine heatwaves, one in January and a second one in February 2020 showed mean temperatures of 1.8 °C above the 20-year climatology values. During the first heatwave, a rapid and strong (60%) decrease in microbial community biomass was observed, Criptophyceae were replaced by unidentified nanophytoflagellates and other heterotrophic groups. The community experienced an increase in heterotrophic metabolism via an increase in community respiration (CR, 12.79 mmolO2 m−3d−1) and a negative net community production (NCP, −14.9 ± 0.31 mmolO2 m−3d−1), leading to a production:respiration (P:R) rate < 1. Additionally, the most representative fatty acids (FAs: 14:0, 16:0, 18:0, 16:1ω9, 18:1ω9, 18:2ω6 and 18:3ω3) decreased, except for the monounsaturated FAs (MUFA) 16:1ω9 and 18:1 ω9, which increased during this first heatwave. In the second marine heatwave, total biomass dropped to the minimum values reported during the entire study. Here, CR was at its maximum (25.09 mmolO2 m−3d−1), but NCP was also positive (1.96 mmolO2 m−3d−1) and P:R > 1, associated with an active autotrophic community. Again, significant lipid damage, a decrease in saturated FAs and ⍵6 polyunsaturated FAs, and an increase in MUFAs occurred. This field study validates previous experimental results on changes in natural plankton composition and physiology under global warming scenarios.

The fate of amino acid and peptide as affected by soil depth and fertilization regime in subtropical paddies

Amino acids and peptides are important regulators of ecosystem functioning due to their potential role as direct nutrient sources for plants and soil microbes. However, the turnover and driving factors of these compounds in agricultural soils remain poorly understood. This study aimed to reveal the short-term fate of 14C-labeled alanine and tri-alanine derived C under flooding conditions of the top (0–20 cm) and sub-horizons (20–40 cm) of subtropical paddy soils taken from four long-term (31 years since treatment) nitrogen (N) fertilization regimes (i.e., without fertilization, NPK, NPK with straw return (NPKS) or with manure (NPKM)). Amino acid mineralization was strongly affected by the N fertilization regime and soil depth, while peptide mineralization was only distinct between soil layers. The average half-life of amino acid and peptide in the topsoil was 8 h across all treatments, which was higher than previously reported in uplands. The microbial turnover of amino acid and peptide was 7–10 times slower in the subsoil than in the topsoil, with a half-life of about 2–3 days. The half-life of amino acid and peptide for the respired pool was strongly associated with soil physicochemical characteristics, the total biomass, and the structure of soil microbial communities. The N fertilization regime and soil depth affected the substrate uptake rate by microorganisms, with greater uptake observed in the NPKS and NPKM treatments and the topsoil. Microbial amino acid uptake was correlated with the biomass of total and individual microbial groups, whereas microbial peptide uptake was associated with the soil microbial community structure and physicochemical characteristics. This suggests that there are various pathways of amino acid and peptide use by microorganisms under flooding conditions. We conclude that microbial mineralization of amino acid and its peptide in paddy soils under flooding conditions is slower than in upland soils, and that microbial uptake of these substrates is related to soil abiotic factors and the biomass and structure of soil microbial community. These findings have important implications for understanding nutrient cycling and ecosystem functioning in agricultural soils.

Effects of tree diversity on soil microbial community in a subtropical forest in Southwest China

Soil microorganisms are crucial for biological diversity and ecosystem processes in terrestrial ecosystems. Plant diversity has been reported to have positive effects on microbial communities. However, further research is required to understand the complex mechanisms that regulate the interactions between plants and soil microorganisms, especially the corresponding variations in soil microbial communities under tree diversity gradients in natural forest ecosystems. Therefore, we conducted a field investigation in a natural subtropical forest and collected 45 soil samples to evaluate how the soil microbial biomass and community diversity (represented by phospholipid fatty acid biomarkers) responded to a tree diversity gradient as well as their associations with plant (root and litter) traits and soil variables. The contents of total PLFAs ranged from 86.4 to 325.5 nmol g−1 soil with an average of 183.2 ± 66.1 nmol g−1 soil across the 45 plots. Tree diversity significantly enhanced microbial biomass and decreased microbial diversity. Hierarchical partitioning analysis revealed that the soil substrates (including inorganic and organic nutrients) were the major determinants of microbial biomass. Structural equation models also demonstrated that the effects of tree diversity on the biomass and diversity of soil microbial communities were mainly dependent on soil substrates and soil water content, respectively. In addition, soil microorganisms may potentially metabolize relatively recalcitrant carbon components under low tree diversity, whereas they tended to utilize labile carbon sources under high tree diversity. Overall, these findings suggested that the soil microbial community biomass and diversity exhibited distinct changes along the tree diversity gradient, and highlighted the key role of soil substrates availability in controlling microbial biomass.

Quantifying the Immediate Response of Soil to Wild Boar (Sus scrofa L.) Grubbing in Mediterranean Olive Orchards

The goals of the current research were to assess the immediate impact of invasive wild boar (Sus scrofa L.) in olive orchards of southern Italy. Over a one-year study, in grubbed and ungrubbed areas, we measured the seasonal changes on the fast soil biological and chemical responses at depths of 0–15 cm and 15–40 cm, and several leaf and fruit characteristics. The impact factor, IFG, was used to quantify the effects of wild boar on individual soil parameters. Grubbing induced an increase in the soil moisture at both depths. Soil pH, organic matter, and C/N ratio were higher in grubbed soils at 0–15 cm and lower at 15–40 cm compared to ungrubbed soils. These trends were reflected in the higher microbial community biomass and the inhibition of fungal fraction in grubbed topsoil, while an opposite tendency at 15–40 cm was found. Microbial biomass had the highest IFG in topsoil (94%) and metabolic quotient (85%) at a 15–40 cm depth. Microbial stress condition and C loss were found in grubbed soil at both depths. Furthermore, these soils were also shown to be of lower quality than ungrubbed soils, especially at 0–15 cm (SQI = 0.40 vs. 0.50, respectively). A stronger negative impact of wild boar grubbing was observed in the Autumn/Winter and for fruit polyphenol content.

The Effects of Trichoderma viride T23 on Rhizosphere Soil Microbial Communities and the Metabolomics of Muskmelon under Continuous Cropping

The continuous cropping can restrict the large scale and intensive cultivation of muskmelon, and the use of Trichoderma preparation to alleviate the negative effects is an effective mean. Although the impact on rhizosphere soil microbial communities and metabolites after applying Trichoderma are still unclear. In this study, we applied the fermentation broth of Trichoderma viride T23 to muskmelon under continuous cropping, collected rhizosphere soil samples at 60 days after transplantation, and investigated the changes in the microbial communities and metabolites of muskmelon by using high−throughput sequencing and metabolomic analysis, respectively. The results showed that T. viride T23 could effectively reduce the disease index of muskmelon wilt (65.86 to 18) and significantly increase the soil pH value (6.06 to 6.40). Trichoderma viride T23 induced drastic shifts in the richness, structure, and composition of rhizosphere microbial communities, and Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant bacterial phyla. Bioactive substances such as scopoletin, erythronic acid, and palmitic acid were significantly upregulated in the rhizosphere soil, which enhanced soil activity. Overall, T. viride T23 resolves the continuous cropping limitation in muskmelon by improving soil physicochemical properties, elevating the biomass and diversity of soil microbial communities, and stimulating the production of soil active substances.

Soil microbial responses to large changes in precipitation with nitrogen deposition in an arid ecosystem.

Climatic change severely affects terrestrial ecosystem functioning by modifying soil microbial communities, especially in arid ecosystems. However, how precipitation patterns affect soil microbes and the underlying mechanisms remain largely unclear, particularly under long-term dry-wet cycling and vice versa in field settings. In this study, a field experiment was conducted to quantify soil microbial responses and resilience to precipitation changes with nitrogen addition. We established five levels of precipitation with nitrogen addition over the first 3 years and then balanced this with compensatory precipitation in the fourth year (i.e., reversed the precipitation treatments), to recover to the levels expected over 4 years in a desert steppe ecosystem. Soil microbial community biomass increased with increasing precipitation, and the reversed precipitation reversed these responses. The soil microbial response ratio was constrained by the initial reduction in precipitation, whereas the resilience and limitation/promotion index of most microbial groups tended to increase. Nitrogen addition reduced the response rates of most microbial groups, depending on the soil depth. The soil microbial response and limitation/promotion index could be distinguished by antecedent soil features. The precipitation regime can regulate the responses of soil microbial communities to climatic change via two potential mechanisms: (1) concurrent nitrogen deposition and (2) soil chemical and biological mediation. Soil microbial behaviors and their associations with soil properties should be considered when assessing the responses of terrestrial ecosystems to climatic change.

Combined effects of long-term tillage and fertilisation regimes on soil organic carbon, microbial biomass, and abundance of the total microbial communities and N-functional guilds

Reduced tillage intensity is known to increase soil organic carbon (SOC) in the topsoil, but can also lead to increased microbially derived nitrous oxide (N2O) emissions. Although the trade-offs between C sequestration and N2O emissions under different agricultural practices have been extensively investigated, the reported results are conflicting and, thus remain unclear. In this study, the effects of different types of tillage [no-till (NT) and conventional mouldboard tillage (CT)] in combination with four fertilisation regimes [unfertilised control (CON), mineral NPK (MIN), organic (compost) (ORG), and mixed (NPK + compost) (MIX)] on SOC and microbial biomass (Cmic) were examined two decades after the experiment was initiated. The abundance of the microbial community and N-functional guilds within the soil profile (up to a depth of 60 cm) was also determined. SOC content was significantly higher in NT than in CT at 0–10 cm depth, with an average difference of 0.6–1.3 % SOC, depending on fertilisation. Organic fertilisation increased the SOC content in both tillage systems up to a depth of 20 cm. Microbial biomass, abundance of total bacterial and archaeal 16S rRNA, and fungal ITS genes decreased with depth, corresponding to the decrease in SOC, and, consequently, were higher in NT than in CT, in the top 20 cm soil for microbial biomass and bacterial abundance and top 10 cm for fungi and archaea. Denitrifiers and ammonium oxidising archaea (AOA) were affected by soil depth and tillage, whereas the distribution of ammonium oxidising bacteria (AOB) was affected by fertilisation and depth. The ratios between (i) the two nitrite-reducing communities (nirS/nirK), (ii) the two N2O-reducing communities (nosZI/nosZII), and (iii) the nitrite- and N2O-reducing communities [(nirK + nirS)/(nosZ + nosZII)] increased significantly with soil depth, indicating niche differentiation caused by differences in nutrients contents and environmental conditions. Overall, stratification of SOC and nutrients in the soil by tillage and fertilisation was the main driver of the differences in the total microbial and N cycling communities. The findings of our study provide novel insights that can aid in development of effective strategies for steering soil microbiome responsible for N2O emissions.

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.

Annual dynamics of indigenous microbial communities of forest soils after severe PAH contamination

Polycyclic aromatic hydrocarbons (PAHs) are worldwide contaminants that, due to their long-range transport, can accumulate far from the emission sources, e.g. in forest soils. Since changes in soil microbial community can have an impact on ecosystem processes (e.g. nutrient cycling, decomposition, stress stability), studies on the succession of indigenous microbial community following exposure to PAHs are important. Most of these studies are limited to soils aged contaminated with PAHs, since our aim was to fill the knowledge gap on recent PAH contamination. To this aim, soils from three forest systems (holm oak, black pine and beech) were spiked with 3 PAHs (phenanthrene, pyrene and benzo[a]pyrene) and incubated under controlled conditions in mesocosm. During the first year after incubation, changes in the activity and biomass of the soil microbial community were estimated by analysing phospholipid fatty acids (PLFA), fungal biomass (ergosterol content), and fungal and bacterial growth. Findings demonstrated that PAHs affected the soil microbial community structure. Actinomycetes, fungi and Gram+-bacteria were initially resistant to PAH contamination in all the forest systems, whereas for fungi a recovery was observed at the end of incubation, such as ergosterol and growth, in holm oak and beech soils. PAH spikes seemed to have an overall negative effect on bacteria and Gram- groups in all the soils at the beginning of incubation. Considering the values of metabolic activity index (MAI), the composition of the microbial community did not seem to be resistant to the addition of PAHs. However, the soil under beech showed a slightly better resistance to contamination. Furthermore, the community structure did not appear to change in relation to the PAH considered. Overall, in the microbial community of holm oak and beech soils, different groups were able to quickly recover from the new soil conditions.