Resource Legacies of Organic and Conventional Management Differentiate Soil Microbial Carbon Use

Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils

Stable soil organic carbon (SOC) formation in coastal saline soils is important to improve arable land quality and mitigate greenhouse gas emissions. However, how microbial life-history strategies and metabolic traits regulate SOC turnover in coastal saline soils remains unknown. Here, we investigated the effects of microbial life history strategy tradeoffs on microbial carbon use efficiency (CUE) and microbial-derived SOC formation using metagenomic sequencing technology in different salinity soils. The results showed that high-salinity is detrimental to microbial CUE and microbial-derived SOC formation. Moreover, the regulation of nutrients stoichiometry could not mitigate adverse effects of salt stress on microbial CUE, which indicated that microbial-derived SOC formation is independent of stoichiometry in high-salinity soil. Low-salinity soil is dominated by a high growth yield (Y) strategy, such as higher microbial biomass carbon and metabolic traits which are related to amino acid metabolism, carbohydrate metabolism, and cell processes. However, high-salinity soil is dominated by stress tolerance (S) (e.g., higher metabolic functions of homologous recombination, base excision repair, biofilm formation, extracellular polysaccharide biosynthesis, and osmolytes production) and resource acquisition (A) strategies (e.g., higher alkaline phosphatase activity, transporters, and flagellar assembly). These trade-offs of strategies implied that resource reallocation took place. The high-salinity soil microbes diverted investments away from growth yield to microbial survival and resource capture, thereby decreasing biomass turnover efficiency and impeding microbial-derived SOC formation. Moreover, altering the stoichiometry in low-salinity soil caused more investment in the A-strategy, such as the production of more β-glucosidase and β-N-acetyl-glucosaminidase, and increasing bacterial chemotaxis, which thereby reduced microbial-derived SOC formation. Our research reveals that shift the microbial community from S- and A- strategies to the Y-strategy is important to increase the microbial CUE, and thus enhance SOC turnover in coastal saline soils.

Soil Health and Biodiversity Is Driven by Intensity of Organic Farming in Canada

Organic farming is continuing to expand in Canada, with close to 6,000 producers farming over 2% of all agricultural land. There is insufficient evidence, however, of a trend toward larger average farm size and increasing specialization by these organic farms. This mini-review postulates that a gradient of intensity of farm management exists within organic farming sectors in Canada, with respect to cropping diversity, and tillage and nutrient utilization, and this gradient of intensity is a key determinant of agroecological outcomes. This variation in management approach and intensity reflects producer's individual perspectives on organic farming principles and practices, irrespective of farm scale. By directly influencing farm crop and vegetative diversity and cover, and farm nutrient status and carbon cycling, management intensity determines soil carbon storage and flux, soil health and biodiversity agroecological and ecosystem services, plus farm agronomic resilience. Demographic trends and perspectives of new entrants in organic farming are encouraging signs of an increasingly inclusive and socio-ecologically complex Canadian organic farming sector, which recognizes the agroecological implications of intensity of organic farm management across all production sectors.

Microbial community structure and functional genes drive soil priming effect following afforestation

Afforestation substantially modifies native soil organic carbon (SOC) decomposition via plant carbon inputs (the priming effect), and in turn, triggers vital biogeochemical processes that influence the regulation of soil carbon dynamics. Soil microbes are crucial in regulating the direction and magnitude of the priming effect. In the present study, we performed metagenomic sequencing and ¹³C-glucose labeling analyses of microbial communities and priming effects across a Robinia pseudoacacia afforestation chronosequence (14-, 20-, 30-, and 45-year-old stands) in the Loess Plateau in China, with adjacent farmland being selected as a control. Our results revealed that the cumulative priming effect across five sites along the afforestation chronosequence initially increased and approached a peak value in the 20-year-old stand, after which it declined. The priming effect was predominantly driven by the microbial community structure (i.e., the fungal-to-bacterial ratios and relative abundances of Proteobacteria and Actinobacteria), and stable C decomposition genes and C-degrading enzymes. Specifically, among the key functional genes correlated with priming effect, which were identified in orders Rhizobiales and Pseudonocardiales, considerably promoted SOC priming. Overall, our findings indicate that afforestation alters soil microbial community structure and function, particularly with respect to enhancing stable soil C decomposition genes, which may promote SOC priming. The findings of the present study could enhance our understanding of fresh C input-induced changes associated with C mineralization in the context of the revegetation of ecologically fragile areas.

Soil Aggregation Shaped the Distribution and Interaction of Bacterial-Fungal Community Based on a 38-Year Fertilization Experiment in China

Soil aggregates provide different ecological niches for microorganisms, and in turn, the microbial interactions affect soil aggregation process. The response of the microbial community in bulk soil to different fertilization regimes has been well studied; however, the co-occurrence patterns of bacteria and fungi in different aggregates under various fertilization regimes remain unclear. Based on the long-term field experiment, we found that fertilization regimes contributed more to fungal than to bacterial community composition. Long-term fertilization decreased microbial interactions in large macroaggregates (LM), macroaggregates (MA) and silt and clay (SC) fractions, but increased in microaggregates (MI). The application of manure with inorganic fertilizers (NPKM) significantly increased the intensive cooperation between bacteria and fungi in LM and MA. Microbial communities in LM and MA were well separated and showed strong competition against microbes in MI and SC; hence, we concluded that the microbial habitat could be divided into two groups, large fractions (LM and MA) and small fractions (MI and SC). The bacterial genera Anaerolinea, Nocardioides, Ohtaekwangia, Geoalkalibacter, Lysobacter, Pedomicrobium, and Flavisolibacter were keystone taxa in inorganic fertilization, and Roseiflexus, Nitrospira, and Blastocatella were keystone taxa in NPKM, which were all sensitive to soil aggregation. In this study, we demonstrated that the NPKM decreased the microbial interactions within and between kingdoms in LM, MA, and SC, but enhanced nutrient availability and microbial interactions in MI, leading to the formation of biofilms and the strengthening of stress tolerance, which finally stimulated the formation and stabilization of soil aggregates. Thus, this study revealed how soil microbial competition or cooperation responded to different fertilization regimes at aggregate scales, and provided evidence for the stimulation of soil stability.

Dynamic Changes in Soil Microbial Communities with Glucose Enrichment in Sediment Microbial Fuel Cells

To investigate soil microbial community dynamics in sediment microbial fuel cells (MFCs), this study applied nonhydric (D) and hydric (S) soils to single-chamber and mediator-free MFCs. Glucose was also used to enrich microorganisms in the soils. The voltage outputs of both the D and S sediment MFCs increased over time but differed from each other. The initial open circuit potentials were 345 and 264 mV for the D and S MFCs. The voltage output reached a maximum of 503 and 604 mV for D and S on days 125 and 131, respectively. The maximum power densities of the D and S MFCs were 2.74 and 2.12 mW m^-2, analyzed on day 50. Clustering results revealed that the two groups did not cluster after glucose supplementation and 126 days of MFC function. The change in Geobacter abundance was consistent with the voltage output, indicating that these bacteria may act as the main exoelectrogens on the anode. Spearman correlation analysis demonstrated that, in the D soils, Geobacter was positively correlated with Dialister and negatively correlated with Bradyrhizobium, Kaistobacter, Pedomicrobium, and Phascolarctobacterium; in the S soils, Geobacter was positively correlated with Shewanella and negatively correlated with Blautia. The results suggested that different soil sources in the MFCs and the addition of glucose as a nutrient produced diverse microbial communities with varying voltage output efficiencies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-021-00959-x.

Agricultural management and cultivation period alter soil enzymatic activity and bacterial diversity in litchi (Litchi chinensis Sonn.) orchards

BACKGROUND

Agricultural management and temporal change including climate conditions and soil properties can result in the alteration of soil enzymatic activity and bacterial community, respectively. Therefore, different agricultural practices have been used globally to explore the soil quality. In this study, the temporal variations in soil property, enzymatic activity, and bacterial community at three successive trimester sampling intervals were performed in the soil samples of litchi orchards that were maintained under conventional and sustainable agricultural practices.

RESULTS

Agricultural management found to significantly influence arylsulfatase, β-glucosidase, and urease activities across time as observed by repeated-measures analysis of variance. Shannon and Simpson diversity indices, and the relative abundance of predominant Acidobacteria and Proteobacteria were significantly influenced by temporal change but not agricultural management. This suggested that soil enzymatic activity was more susceptible to the interaction of temporal change and agricultural management than that of the bacterial community. Multiple regression analysis identified total nitrogen, EC, and phosphorus as the significant predictors of acid phosphatase, arylsulfatase, and β-glucosidase for explaining 29.5-39% of the variation. Moreover, the soil pH and EC were selected for the SOBS, Chao, ACE, and Shannon index to describe 33.8%, 79% of the variation, but no significant predictor was observed in the dominant bacterial phyla. Additionally, the temporal change involved in the soil properties had a greater effect on bacterial richness and diversity, and enzymatic activity than that of the dominant phyla of bacteria.

CONCLUSIONS

A long-term sustainable agriculture in litchi orchards would also decrease soil pH and phosphorus, resulting in low β-glucosidase and urease activity, bacterial richness, and diversity. Nevertheless, application of chemical fertilizer could facilitate the soil acidification and lead to adverse effects on soil quality. The relationship between bacterial structure and biologically-driven ecological processes can be explored by the cross-over analysis of enzymatic activity, soil properties and bacterial composition.

Agricultural management practices influence the soil enzyme activity and bacterial community structure in tea plantations

BACKGROUND

The soil quality and health of the tea plantations are dependent on agriculture management practices, and long-term chemical fertilizer use is implicated in soil decline. Hence, several sustainable practices are used to improve and maintain the soil quality. Here, in this study, changes in soil properties, enzymatic activity, and dysbiosis in bacterial community composition were compared using three agricultural management practices, namely conventional (CA), sustainable (SA), and transformational agriculture (TA) in the tea plantation during 2016 and 2017 period. Soil samples at two-months intervals were collected and analyzed.

RESULTS

The results of the enzyme activities revealed that acid phosphatase, arylsulfatase, β-glucosidase, and urease activities differed considerably among the soils representing the three management practices. Combining the redundancy and multiple regression analysis, the change in the arylsulfatase activity was explained by soil pH as a significant predictor in the SA soils. The soil bacterial community was predominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Bacteroidetes in the soil throughout the sampling period. Higher Alpha diversity scores indicated increased bacterial abundance and diversity in the SA soils. A significant relationship between bacterial richness indices (SOBS, Chao and ACE) and soil pH, K and, P was observed in the SA soils. The diversity indices namely Shannon and Simpson also showed variations, suggesting the shift in the diversity of less abundant and more common species. Furthermore, the agricultural management practices, soil pH fluctuation, and the extractable elements had a greater influence on bacterial structure than that of temporal change.

CONCLUSIONS

Based on the cross-over analysis of the bacterial composition, enzymatic activity, and soil properties, the relationship between bacterial composition and biologically-driven ecological processes can be identified as indicators of sustainability for the tea plantation.

Living in the plastic age - Different short-term microbial response to microplastics addition to arable soils with contrasting soil organic matter content and farm management legacy

Microplastics (MPs) are an emerging pollutant found in many ecosystems including soils, where they may become toxic to organisms or alter their habitat. However, little is known about the influence of MPs on soil microorganisms and processes vital to ecosystem functioning in different soils. Therefore, our objective was to investigate the short-term effects of MPs pollution on soil microorganisms in two agricultural soils with contrasting soil organic matter content and microbial biomass as caused by farm management history (organic and conventional). Soils were amended with two kinds of raw MPs particles, low-density polyethylene (LDPE) and polypropylene (PP) in the size range of 200-630 μm at a rate of 1% w/w and incubated for 28 days. During incubation, microbial respiration was determined. After incubation, the microbial biomass carbon (C) and nitrogen (N), gene copy numbers of archaea, bacteria and fungi were quantified and extractions performed to gauge effects on C and N mineralisation. The results of this study showed no major detrimental effects of MPs on microbial activity. However, in particular PP reduced microbial biomass in both soils, with a stronger decline in the organic soil, showing lower resistance to MPs. Nevertheless, mineralisation processes remained on the same level, showing functional resistance of the microbial community to MPs addition in both soils. The microbial community composition was not significantly altered by MPs addition, even though fungi tended to decrease in the organic soil. Overall, management legacy had a stronger effect on soil microorganisms, with higher microbial biomass and activity in the organic soil. While this study does not answer whether MPs pollution has a negative impact on soil microorganisms, it highlights the need to consider potential interactive effects of environmental factors, land use and management with MPs on soil microbial communities and their functions.

Effect of the amount of organic trigger compounds, nitrogen and soil microbial biomass on the magnitude of priming of soil organic matter

Priming effects (PEs) are defined as short-term changes in the turnover of soil organic matter (SOM) caused by the addition of easily degradable organic compounds to the soil. PEs are ubiquitous but the direction (acceleration or retardation of SOM decomposition) and magnitude are not easy to predict. It has been suggested that the ratio between the amount of added PE-triggering substrate to the size of initial soil microbial biomass is an important factor influencing PEs. However, this is mainly based on comparison of different studies and not on direct experimentation. The aim of the current study is to examine the impact of glucose-to-microbial biomass ratios on PEs for three different ecosystems. We did this by adding three different amounts of ¹³C-glucose with or without addition of mineral N (NH₄NO₃) to soils collected from arable lands, grasslands and forests. The addition of ¹³C-glucose was equivalent to 15%, 50% and 200% of microbial biomass C. After one month of incubation, glucose had induced positive PEs for almost all the treatments, with differences in magnitude related to the soil origin and the amount of glucose added. For arable and forest soils, the primed C increased with increasing amount of glucose added, whereas for grassland soils this relationship was negative. We found positive correlations between glucose-derived C and primed C and the strength of these correlations was different among the three ecosystems considered. Generally, additions of mineral N next to glucose (C:N = 15:1) had little effect on the flux of substrate-derived C and primed C. Overall, our study does not support the hypothesis that the trigger-substrate to microbial biomass ratio can be an important predictor of PEs. Rather our results indicate that the amount of energy obtained from decomposing trigger substrates is an important factor for the magnitude of PEs.

Energy use efficiency of root growth - a theoretical bioenergetics framework

Metabolic efficiency of root growth is a crucial physiological parameter, contributing to the amount of photosynthate that plants need to invest into soil exploration. Common measurements of metabolic efficiency usually rely on CO₂ respiration measurements with the underlying assumption that all metabolic processes are taking place under aerobic conditions. In this conceptual paper, we introduce energy use efficiency based on the quantification of heat dissipation and energy fluxes as an alternative metric to quantify the metabolic efficiency of root growth. In a theoretical framework, we adopted recently published heat dissipation data from wheat seedlings and show that energy use efficiency decreases in response to (i) soil hypoxia and (ii) increased soil penetration resistance. In contrast to traditional CO₂ respiration measurements, heat dissipation measurements account for both aerobic as well as anaerobic respiration in growing roots. Hence, we advocate that the quantification of heat dissipation provides a more complete picture of the metabolic efficiency of root growth than CO₂ respiration measurements alone. We therefore propose that energy use efficiency should be included in future studies assessing the metabolic efficiency of root growth.

Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa

Soil microbes have critical influence on the productivity and sustainability of agricultural ecosystems, yet the magnitude and direction to which management practices affect the soil microbial community remain unclear. This work aimed to examine the impacts of three farming systems, conventional grain cropping (CON), organic grain cropping (ORG), and grain cropping-pasture rotation (ICL), on the soil microbial community structure and putative gene abundances of N transformations using high-throughput 16S rRNA gene and ITS sequencing approaches. Two additional systems, a forest plantation (PF) and an abandoned agricultural field subject to natural succession (SUC), were also included for better assessment of the soil microbial community in terms of variation scale and regulatory importance of management intensity vs. plant type. Farming systems significantly affected the biodiversity of soil fungi but not bacteria, with Shannon index being the lowest in ORG. Bacterial and fungal communities in three cropping systems clustered and separated from those in PF and SUC, suggesting that management practices as such played minor roles in shaping the soil microbial community compared to plant type (i.e., woody vs. herbaceous plants). However, management practices prominently regulated habitat-specific taxa. Lecanoromycetes, a class of Ascomycota accounted for ∼10% of total fungal population in ORG, but almost nil in the other four systems. ORG also enriched bacteria belonging to the phyla, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Gemmatimonadetes. Further, PICRUSt predicted that N-cycle community compositions varied with farming systems; compared to CON, ORG and ICL were more divergent from PF and SUC. Soil pH, together with inorganic N, extractable organic C, and soil organic C:N ratio explained < 50% of the total variations in both bacterial and fungal communities. Our data indicates that while moderately affecting the overall structure of the soil microbial community, management practices, particularly fertilization and the source of N (synthetic vs. organic), were important in regulating the presence and abundance of habitat-specific taxa.