Organic Carbon Mineralization and Bacterial Community of Active Layer Soils Response to Short-Term Warming in the Great Hing'an Mountains of Northeast China

Soil Parameters and Forest Structure Commonly Form the Microbiome Composition and Activity of Topsoil Layers in Planted Forests

Soil bacterial communities play a remarkable role in nutrient cycling, significantly affecting soil organic material content, soil fertility, and, in an indirect way, plant succession processes. Conversely, vegetation type influences microbial soil life. The present study compared the bacterial microbiome composition, diversity and catabolic activity profile of topsoil samples collected under three different forest types (a twice-coppiced black locust stand, a young, naturally reforested, and a middle-aged mixed pedunculate oak stand) planted on former arable land in the early 20th century. Diversity indices determined during 16S ribosomal RNA sequencing-based metagenome analysis indicated that the black locust stand had the highest soil bacterial community diversity. At the phylum level, Acidobacteriota, Actinobacteriota, Proteobacteria, Verrucomicrobiota, Bacteroidota, and Gemmatimonadota were the most abundant taxa in the forest soils. Concerning soil parameters, redundancy analysis revealed that pH had the highest impact on bacterial community structure and pH, and soil organic carbon content on the samples' respiration patterns. As for catabolic activity, the recently clearcut oak forest showed the lowest substrate-induced respiration, and citrate was the main driver for the inter-stand variability of microbial activity. Our results confirm that soil parameters and forest type influence the composition and functioning of the soil bacterial microbiome.

Effects of simulated warming on soil microbial community diversity and composition across diverse ecosystems

Soil warming can directly affect the microbial community, or indirectly affect the microbial community by affecting soil moisture, nutrient availability, vegetation growth, etc. However, the response of microorganisms to soil warming is complex, and there is no uniform conclusion on the impact and mechanism of warming on microbial diversity. As the global climate gradually warms, a comprehensive assessment of warming on soil microbial community changes is essential to understand and predict the response of microbial geochemical processes to soil warming. Here, we perform a meta-analysis of studies to investigate changes in soil microbial communities along soil warming gradients and the response of soil microbes to elevated temperature in different ecosystems. We found that the α diversity index of soil microorganisms decreased significantly with the increase in temperature, and the β diversity altered with the increase in soil temperature and the shifts in ecosystem. Most bacteria only alter when the temperature rises higher. Compared to the non-warming condition, the relative abundance of Acidobacteria, Proteobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia decreased by 19 %, 11 %, 19 %, 8 % and 6 %, respectively, and the relative abundance of Firmicutes increased by 34 %. Compared to farmland, forest, grassland and tundra ecosystems, soil microorganisms in wetland ecosystems were more sensitive to temperature increase, and the changes in bacteria were consistent with the overall alterations. This meta-analysis revealed significant changes in the composition of microbial communities on soil warming. With the decrease in biodiversity under increasing temperature conditions, these dominant microbiomes, which can grow well under high-temperature conditions, will play a stronger role in regulating nutrient and energy flow. Our analysis adds a global perspective to the temperature response of soil microbes, which is critical to improving our understanding of the mechanisms of how soil microbes change in response to climate warming.

Unveiling the crucial role of soil microorganisms in carbon cycling: A review

Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.

Warming effects on grassland soil microbial communities are amplified in cool months

Global warming modulates soil respiration (RS) via microbial decomposition, which is seasonally dependent. Yet, the magnitude and direction of this modulation remain unclear, partly owing to the lack of knowledge on how microorganisms respond to seasonal changes. Here, we investigated the temporal dynamics of soil microbial communities over 12 consecutive months under experimental warming in a tallgrass prairie ecosystem. The interplay between warming and time altered (P < 0.05) the taxonomic and functional compositions of microbial communities. During the cool months (January to February and October to December), warming induced a soil microbiome with a higher genomic potential for carbon decomposition, community-level ribosomal RNA operon (rrn) copy numbers, and microbial metabolic quotients, suggesting that warming stimulated fast-growing microorganisms that enhanced carbon decomposition. Modeling analyses further showed that warming reduced the temperature sensitivity of microbial carbon use efficiency (CUE) by 28.7% when monthly average temperature was low, resulting in lower microbial CUE and higher heterotrophic respiration (Rh) potentials. Structural equation modeling showed that warming modulated both Rh and RS directly by altering soil temperature and indirectly by influencing microbial community traits, soil moisture, nitrate content, soil pH, and gross primary productivity. The modulation of Rh by warming was more pronounced in cooler months compared to warmer ones. Together, our findings reveal distinct warming-induced effects on microbial functional traits in cool months, challenging the norm of soil sampling only in the peak growing season, and advancing our mechanistic understanding of the seasonal pattern of RS and Rh sensitivity to warming.

Analysis of microbial communities in solid and liquid pig manure during the fertilization process

Utilizing livestock manure as organic fertilizer in sustainable agriculture is crucial and should be developed through an appropriate manufacturing process. Solid-liquid separation contributes to reducing odor, managing nutrients in livestock excretions, and lowering the cost of transporting manure to arable soil. To investigate the impact of fermentation after solid-liquid separation, we examined the specific correlation between chemical properties and bacterial communities in solid-liquid manures before and after the fermentation process. In terms of chemical properties before fermentation, the levels of electrical conductivity, nitrogen, ammonium nitrogen (NH4+-N), potassium, sodium, and chloride were higher in the liquid sample than in the solid sample. However, the chemical components of the liquid sample decreased during fermentation, which could be attributed to the low organic matter content. Many chemical components increased in the solid samples during fermentation. Fifty-six bacterial species were significantly correlated with NH4+-N and phosphorus. Following fermentation, their abundance increased in the solid samples and decreased in the liquid samples, indicating the potential for NH4+-N release or phosphorus mineralization from organic matter. These results provide information regarding changes in nutrient and bacterial formation when applying the fermentation process after solid-liquid separation.

Gut microbial communities and their potential roles in cellulose digestion and thermal adaptation of earthworms

Adaptations to temperature and food resources, which can be affected by gut microbiota, are two main adaptive strategies allowing soil fauna to survive in their habitats, especially for cold-blooded animals. Earthworms are often referred to as ecosystem engineers because they make up the biggest component of the animal biomass found in the soil. They are considered as an important indicator in the triangle of soil quality, health and functions. However, the roles of gut microbiota in the environmental adaptation of earthworms at a large scale remain obscure. We explored the gut bacterial communities and their functions in the environmental adaptation of two widespread earthworm species (Eisenia nordenskioldi Eisen and Drawida ghilarovi Gates) in Northeast China (1661 km). Based on our findings, the alpha diversity of gut bacterial communities decreased with the increase of latitude, and the gut bacterial community composition was shaped by both mean annual temperature (MAT) and cellulose. Actinobacteria, Proteobacteria, Firmicutes, and Planctomycetes, recognized as the predominant cellulose degraders, were keystone taxa driving gut bacterial interactions. Actinobacteria, Firmicutes, and Planctomycetes were influenced by MAT and cellulose, and had higher contributions to gut total cellulase activity. The optimal temperature for total cellulase in the gut of E. nordenskioldi (25-30 °C) was lower than that of D ghilarovi (40 °C). The gut microbiota-deleted earthworms had the lowest cellulose degradation rate (1.07 %). The cellulose was degraded faster by gut bacteria from the host they were derived, indicating the presence of home field advantage of cellulose decomposition. This study provides a foundation for understanding the biotic strategies adopted by earthworms when they enter a new habitat, with gut microbiota being central to food digestion and environmental adaptability.

Organic vs. conventional: impact of cultivation treatments on the soil microbiota in the vineyard

The aim of this study was to compare the effects of two vineyard management practices on the soil and its associated microbiota. The experiments were conducted in two adjacent plots, one completely organically managed and the other conventionally managed in terms of phytosanitary treatments but fertilized with organic amendments. The chemical soil analyses were correlated to the prokaryotic and fungal communities, which were studied using the metabarcoding technique. The main difference between the two treatments was a significantly higher amount of Cu in the organic managed vineyard soil, while conventional managed soil presented higher concentration of Na and Mg and was also associated with higher pH values. Despite these differences, no significant diversities were observed on soil biodiversity and microbial composition considering alpha and beta diversity metrics. However, the percentages of some phyla analyzed individually differed significantly between the two managements. Analyzing the metabolisms of these phyla, it was discovered an increment of species correlated to soils with higher organic matter content or land not used for agricultural purposes in the organic treated soil. The findings indicate that, despite the use of copper-based phytosanitary products, there was no degradation and loss of biodiversity in the organic soil microbial population compared to conventional management with the same type of fertilization, and the observed microbial population was more similar to that of natural soils.

Warming changes the composition and diversity of fungal communities in permafrost

Purpose

It is the data support and theoretical basis for the response mechanism of soil fungi to climate warming in permafrost areas in the Greater Xing’an Mountains.

Methods

We collected permafrost from the Greater Xing’an Mountains for indoor simulation experiments and took the natural permafrost as the control (CK) and the test groups of 0 °C (T1), 2 °C (T2), and 4 °C (T3) were set. Illumina MiSeq high-throughput sequencing technology was used to understand the changes in characteristics of fungal communities, and the correlations were analyzed combined with the soil physicochemical properties.

Results

Compared with CK, the value of pH and the content of available potassium (AK) in the three warming treatment groups were significantly lower (P < 0.05), and the microbial biomass carbon (MBC) content was significantly higher (P < 0.05). The content of total nitrogen (TN) and available nitrogen (AN) in the T1 and T3 groups was significantly lower than that in the CK group (P < 0.05). A total of 11 phyla, 39 classes, 89 orders, 187 families, 361 genera, and 522 species were obtained through fungal sequencing and divided into 1463 amplicon sequence variants (ASVs). Ascomycota and Dimorphospora were the dominant phylum and genus, respectively, and there were differences in the response of relative abundance of various groups at the phylum and genus levels to warming. Warming significantly decreased the Sobs and ACE indexes of the treatment groups (P < 0.05), and the Shannon and Shannoneven indexes also showed a downward trend. Moreover, warming significantly changed the fungal beta diversity (P < 0.01), while the value of pH and the content of TN, MBC, and AK could significantly affect the community structure (P < 0.05), and the correlation between fungi at different phyla levels and soil physicochemical properties was different.

Conclusions

These results can provide a reference for further study on the changes in composition and structure of fungal communities and the influence factor in permafrost in the Greater Xing’an Mountains under the background of warming.

Response of Carbon Emissions and the Bacterial Community to Freeze-Thaw Cycles in a Permafrost-Affected Forest-Wetland Ecotone in Northeast China

Climate warming can affect freeze–thaw cycle (FTCs) patterns in northern high-latitude regions and may affect permafrost carbon emissions. The response of carbon release and microbial communities to FTCs has not been well characterized. Here, we conducted laboratory incubation experiments to investigate the relationships among carbon emissions, bacterial community, and soil variables in a permafrost-affected forest–wetland ecotone in Northeast China. The emission rates of CO₂ and CH₄ increased during the FTCs. FTC amplitude, FTC frequency, and patch type had significant effects on carbon emissions. FTCs increased the contents of soil DOC, NH₄⁺-N, and NO₃⁻-N but reduced bacterial alpha diversity. CO₂ emissions were mainly affected by bacterial alpha diversity and composition, and the inorganic nitrogen content was the important factor affecting CH₄ emissions. Our findings indicated that FTCs could significantly regulate CO₂ and CH₄ emissions by reducing bacterial community diversity and increasing the concentration of available soil substrates. Our findings shed new light on the microorganism-substrate mechanisms regulating the response patterns of the soil carbon cycle to FTCs in permafrost regions.

Spatial Variation of Microbial Community Structure and Its Driving Environmental Factors in Two Forest Types in Permafrost Region of Greater Xing′an Mountains

Climate warming is accelerating permafrost degradation. Soil microorganisms play key roles in the maintenance of high-latitude permafrost regions and forest ecosystems’ functioning and regulation of biogeochemical cycles. In this study, we used Illumina MiSeq high-throughput sequencing to investigate soil bacterial community composition at a primeval Larix gmelinii forest and a secondary Betula platyphylla forest in a permafrost region of the Greater Xing’an Mountains. The Shannon diversity index tended to decrease and then increase with increasing soil depth, which was significantly higher in the L. gmelinii forest than in the B. platyphylla forest at 40–60 cm. Proteobacteria (19.86–29.68%), Acidobacteria (13.59–31.44%), Chloroflexi (11.04–27.19%), Actinobacteria (7.05–25.57%), Gemmatimonadetes (1.76–9.18%), and Verrucomicrobia (2.03–7.00%) were the predominant phyla of the bacterial community in two forest types. The relative abundance of Proteobacteria showed a decreasing trend in the B. platyphylla forest and an increasing trend in the L. gmelinii forest, whereas that of Chloroflexi increased and then decreased in the B. platyphylla forest and decreased in the L. gmelinii forest with increasing soil depth. The relative abundance of Acidobacteria was significantly higher in the B. platyphylla forest than in the L. gmelinii forest at 0–20 cm depth, whereas that of Actinobacteria was significantly higher in the L. gmelinii forest than in the B. platyphylla forest at 0–20 cm and 40–60 cm depth. Principal coordinate analysis (PCoA) and two-way analysis of variance (ANOVA) indicated that microbial community composition was more significantly influenced by forest type than soil depth. Redundancy analysis (RDA) showed that microbial community structure was strongly affected by soil physicochemical properties such as nitrate nitrogen (NO3−-N), pH, and total organic carbon (TOC). These results offer insights into the potential relationship between soil microbial community and forest conversion in high latitude permafrost ecosystems.

Plant-Microbe Interaction in Sustainable Agriculture: The Factors That May Influence the Efficacy of PGPM Application

The indiscriminate use of chemical fertilizers and pesticides has caused considerable environmental damage over the years. However, the growing demand for food in the coming years and decades requires the use of increasingly productive and efficient agriculture. Several studies carried out in recent years have shown how the application of plant growth-promoting microbes (PGPMs) can be a valid substitute for chemical industry products and represent a valid eco-friendly alternative. However, because of the complexity of interactions created with the numerous biotic and abiotic factors (i.e., environment, soil, interactions between microorganisms, etc.), the different formulates often show variable effects. In this review, we analyze the main factors that influence the effectiveness of PGPM applications and some of the applications that make them a useful tool for agroecological transition.