Effects of plant-symbiotic relationships on the living soil microbial community and microbial necromass in a long-term agro-ecosystem

Divergent assembly of soil microbial necromass from microbial and organic fertilizers in Chimonobambusa hejiangensis forest

Introduction

Variability in microbial residues within soil aggregates are becoming progressively essential to the nutritive and sustainability of soils, and are therefore broadly regarded as an indispensable part of soil organic matter. It is unexplored how the widespread implementation of microbial fertilisers in agricultural production impacts soil organic nutrients, in particular the microbial residue fraction.

Methods

We performed a three-year field experiment to verify the distinct impacts of microbial and organic fertilizers on carbon accumulation in soil microbial leftovers among aggregate fractions.

Results

Microbial residual carbon was shown to decrease insignificantly during the application of microbial fertilizer and to rise marginally afterwards with the utilization of organic fertilizer. However, the combined effects of the two fertilizers had substantial impacts on the accumulation of microbial residual carbon. Changes in the structure of the fungi and bacteria shown in this study have implications for the short-term potential of microbial fertilizer shortages to permanent soil carbon sequestration. Additionally, our findings revealed variations in microbial residue accumulation across the microbial fertilizers, with Azotobacter chroococcum fertilizer being preferable to Bacillus mucilaginosus fertilizer due to its higher efficiency. In this scenario of nutrient addition, fungal residues may serve as the primary binding component or focal point for the production of new microaggregates, since the quantity of SOC provided by fungal residues increased while that supplied by bacterial residues decreased.

Discussion

Our findings collectively suggested that the mechanisms behind the observed bacterial and fungal MRC (microbial residue carbon) responses to microbial fertilizer or organic fertilizer in bamboo forest soils are likely to be distinct. The application of microbial fertilizers for a limited duration led to a decline soil stable carbon pool, potentially influencing the regulation of soil nutrients in such hilly bamboo forests.

Global synthesis on the response of soil microbial necromass carbon to climate-smart agriculture

Climate-smart agriculture (CSA) supports the sustainability of crop production and food security, and benefiting soil carbon storage. Despite the critical importance of microorganisms in the carbon cycle, systematic investigations on the influence of CSA on soil microbial necromass carbon and its driving factors are still limited. We evaluated 472 observations from 73 peer-reviewed articles to show that, compared to conventional practice, CSA generally increased soil microbial necromass carbon concentrations by 18.24%. These benefits to soil microbial necromass carbon, as assessed by amino sugar biomarkers, are complex and influenced by a variety of soil, climatic, spatial, and biological factors. Changes in living microbial biomass are the most significant predictor of total, fungal, and bacterial necromass carbon affected by CSA; in 61.9%-67.3% of paired observations, the CSA measures simultaneously increased living microbial biomass and microbial necromass carbon. Land restoration and nutrient management therein largely promoted microbial necromass carbon storage, while cover crop has a minor effect. Additionally, the effects were directly influenced by elevation and mean annual temperature, and indirectly by soil texture and initial organic carbon content. In the optimal scenario, the potential global carbon accrual rate of CSA through microbial necromass is approximately 980 Mt C year-1, assuming organic amendment is included following conservation tillage and appropriate land restoration. In conclusion, our study suggests that increasing soil microbial necromass carbon through CSA provides a vital way of mitigating carbon loss. This emphasizes the invisible yet significant influence of soil microbial anabolic activity on global carbon dynamics.

The effectiveness of sewage sludge biochar amendment with Boehmeria nivea L. in improving physicochemical properties and rehabilitating microbial communities in mine tailings

Biochar amendment can be adopted to improve soil substrate, in turn facilitated phytoremediation. However, improvements to the properties of tailings following different feedstocks of biochar amendment in phytoremediation, particularly the impacts on nitrogen cycle and the related nitrogen-fixing microorganisms remain unclear. In this study, a 100-day pot experiment was designed to determine the co-effects of different combinations of woody and non-woody biochar, namely hibiscus cannabinus core biochar (HB), sewage sludge biochar (SB), chicken manure biochar (MB) and two crops (Cassia alata L., Boehmeria nivea L.). It was found that, on the one hand, biochar amendment directly immobilized heavy metal (loid) contamination in the tailings; on the other hand, biochar amendment, particularly non-woody SB, improved soil properties (i.e., the combination of SB with crops increased the total nitrogen content by 4.7-7.5 times). This indirectly improved phytostabilization (i.e., SB increased crop height 1.5-1.8 fold, root length 3.3-3.7 fold, decreased NH4NO3-extractable Pb, Cu, Cd and also increased the relative abundance of nitrogen-fixing bacteria such as Mesorhizobium, Bradyrhizobium, and Rhizobium). Besides this, redundant analysis shown that the carbon, nitrogen sources, and pH provided by the biochar were identified as the key factors associated with the nitrogen-fixing bacteria. Through the comprehensive evaluation of different biochar amendment in phytoremediation, it was found that the non-woody SB got higher comprehensive score (3.1-3.6) in biochar amendment in phytoremediation, especially in Boehmeria nivea L. Thus, the combination of non-woody SB and Boehmeria nivea L. improved microbial function, while the microorganisms in turn promoted crop growth. Our results revealed the prospect of using non-woody SB assisted Boehmeria nivea L. for phytoremediation in multi-metal mine tailings.

Rice-crayfish co-culture increases microbial necromass' contribution to the soil nitrogen pool

The rice-crayfish co-culture (RC) is a putative sustainable agricultural system. However, studies on the ecological effects of long-term RC systems were still lacking. Here, we compare enzymatic stoichiometry, microbial necromass, and microbial community between the RC and rice monoculture systems (RM). Soil enzymatic stoichiometry analysis showed that after transformation from RM to RC for about three years, ammonium nitrogen (NH₄⁺-N) availability increased to depress relative N-acquiring enzyme production, especially for leucine aminopeptidase. The contents of microbial necromass increased approximately onefold in the RC system, making microbial necromass' contribution to the soil nitrogen (N) reach up to 46.72%. Elevation in NH₄⁺ decreased N-acquiring enzyme, and a relatively more effective C acquisition likely benefited microbial necromass retention and production in the RC system. This study highlights that the rice-crayfish co-culture could modify the N pool of the surface paddy soil.

Soil carbon sequestration - An interplay between soil microbial community and soil organic matter dynamics

Soil carbon sequestration (SCS) refers to the uptake of carbon (C) containing substances from the atmosphere and its storage in soil C pools. Soil microbial community (SMC) play a major role in C cycling and their activity has been considered as the main driver of differences in the potential to store C in soils. The composition of the SMC is crucial for the maintenance of soil ecosystem services, as the structure and activity of SMC also regulates the turnover and delivery of nutrients, as well as the rate of decomposition of soil organic matter (SOM). Quantifying the impact of agricultural practices on both SMC and SCS is key to improve sustainability of soil management. Hence, we discuss the impact of farming practices improving SCS by altering SMC, SOM, and soil aggregates, unraveling their inter-and intra-relationships. Using quantitative and process driven insights from 197 peer-reviewed publications leads to the conclusion that the net benefits from agricultural management to improve SCS would not be sustainable if we overlook the role of soil microbial community. Reintroduction of the decayed microbial community to agricultural soils is crucial for enhancing long-term C storage potential of soils and stabilize them over time. The interactions among SMC, SOM, soil aggregates, and agricultural activities still require more knowledge and research to understand their full contribution to the SCS.

Balance between geographic, soil, and host tree parameters to shape soil microbiomes associated to clonal oak varies across soil zones along a European North-South transect

Tree root-associated microbiomes are shaped by geographic, soil physico-chemical, and host tree parameters. However, their respective impacts on microbiome variations in soils across larger spatial scales remain weakly studied. We out-planted saplings of oak clone DF159 (Quercus robur L.) as phytometer in four grassland field sites along a European North-South transect. After four years, we first compared the soil microbiomes of the tree root zone (RZ) and the tree root-free zone (RFZ). Then, we separately considered the total microbiomes of both zones, besides the microbiome with significant affinity to the RZ and compared their variability along the transect. Variations within the microbiome of the tree RFZ were shaped by geographic and soil physico-chemical changes, whereby bacteria responded more than fungi. Variations within both microbiomes of the tree RZ depended on the host tree and abiotic parameters. Based on perMANOVA and Mantel correlation tests, impacts of site specificities and geographic distance strongly decreased for the tree RZ affine microbiome. This pattern was more pronounced for fungi than bacteria. Shaping the microbiome of the soil zones in root proximity might be a mechanism mediating the acclimation of oaks to a wide range of environmental conditions across geographic regions.

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact

Tree roots attract their associated microbial partners from the local soil community. Accordingly, tree root-associated microbial communities are shaped by both the host tree and local environmental variables. To rationally compare the magnitude of environmental conditions and host tree impact, the "PhytOakmeter" project planted clonal oak saplings (Quercus robur L., clone DF159) as phytometers into different field sites that are within a close geographic space across the Central German lowland region. The PhytOakmeters were produced via micro-propagation to maintain their genetic identity. The current study analyzed the microbial communities in the PhytOakmeter root zone vs. the tree root-free zone of soil two years after out-planting the trees. Soil DNA was extracted, 16S and ITS2 genes were respectively amplified for bacteria and fungi, and sequenced using Illumina MiSeq technology. The obtained microbial communities were analyzed in relation to soil chemistry and weather data as environmental conditions, and the host tree growth. Although microbial diversity in soils of the tree root zone was similar among the field sites, the community structure was site-specific. Likewise, within respective sites, the microbial diversity between PhytOakmeter root and root-free zones was comparable. The number of microbial species exclusive to either zone, however, was higher in the host tree root zone than in the tree root-free zone. PhytOakmeter "core" and "site-specific" microbiomes were identified and attributed to the host tree selection effect and/or to the ambient conditions of the sites, respectively. The identified PhytOakmeter root zone-associated microbiome predominantly included ectomycorrhizal fungi, yeasts and saprotrophs. Soil pH, soil organic matter, and soil temperature were significantly correlated with the microbial diversity and/or community structure. Although the host tree contributed to shape the soil microbial communities, its effect was surpassed by the impact of environmental factors. The current study helps to understand site-specific microbe recruitment processes by young host trees.

Non-symbiotic soil microbes are more strongly influenced by altered tree biodiversity than arbuscular mycorrhizal fungi during initial forest establishment

While the relationship between plant and microbial diversity has been well studied in grasslands, less is known about similar relationships in forests, especially for obligately symbiotic arbuscular mycorrhizal (AM) fungi. To assess the effect of varying tree diversity on microbial alpha- and beta-diversity, we sampled soil from plots in a high-density tree diversity experiment in Minnesota, USA, 3 years after establishment. About 3 of 12 tree species are AM hosts; the other 9 primarily associate with ectomycorrhizal fungi. We used phospho- and neutral lipid fatty acid analysis to characterize the biomass and functional identity of the whole soil bacterial and fungal community and high throughput sequencing to identify the species-level richness and composition of the AM fungal community. We found that plots of differing tree composition had different bacterial and fungal communities; plots with conifers, and especially Juniperus virginiana, had lower densities of several bacterial groups. In contrast, plots with a higher density or diversity of AM hosts showed no sign of greater AM fungal abundance or diversity. Our results indicate that early responses to plant diversity vary considerably across microbial groups, with AM fungal communities potentially requiring longer timescales to respond to changes in host tree diversity.

Autotrophic and symbiotic diazotrophs dominate nitrogen-fixing communities in Tibetan grassland soils

Biological nitrogen fixation, conducted by soil diazotrophs, is the primary nitrogen source for natural grasslands. However, the diazotrophs in grassland soils are still far from fully investigated. Particularly, their regional-scale distribution patterns have never been systematically examined. Here, soils (0-5 cm) were sampled from 54 grasslands on the Tibetan Plateau to examine the diazotroph abundance, diversity, and community composition, as well as their distribution patterns and driving factors. The diazotroph abundance was expressed as nifH gene copies, measured using real-time PCR. The diversity and community composition of diazotrophs were analyzed through MiSeq sequencing of nifH genes. The results showed that Cyanobacteria (47.94%) and Proteobacteria (45.20%) dominated the soil diazotroph communities. Most Cyanobacteria were classified as Nostocales which are main components of biological crusts. Rhizobiales, most of which were identified as potential symbiotic diazotrophs, were also abundant in approximately half of the soil samples. The soil diazotroph abundance, diversity, and community composition followed the distribution patterns in line with mean annual precipitation. Moreover, they also showed significant correlations with prokaryotic abundance, plant biomass, vegetation cover, soil pH values, and soil nutrient contents. Among these environmental factors, the soil moisture, organic carbon, available phosphorus, and inorganic nitrogen contents could be the main drivers of diazotroph distribution due to their strong correlations with diazotroph indices. These findings suggest that autotrophic and symbiotic diazotrophs are the predominant nitrogen fixers in Tibetan grassland soils, and highlight the key roles of water and nutrient availability in determining the soil diazotroph distribution on the Tibetan Plateau.