Quantitative assessment of microbial necromass contribution to soil organic matter

C-STABILITY an innovative modeling framework to leverage the continuous representation of organic matter

The understanding of soil organic matter (SOM) dynamics has considerably advanced in recent years. It was previously assumed that most SOM consisted of recalcitrant compounds, whereas the emerging view considers SOM as a range of polymers continuously processed into smaller molecules by decomposer enzymes. Mainstreaming this new paradigm in current models is challenging because of their ill-adapted framework. We propose the C-STABILITY model to resolve this issue. Its innovative framework combines compartmental and continuous modeling approaches to accurately reproduce SOM cycling processes. C-STABILITY emphasizes the influence of substrate accessibility on SOM turnover and makes enzymatic and microbial biotransformations of substrate explicit. Theoretical simulations provide new insights on how depolymerization and decomposers ecology impact organic matter chemistry and amount during decomposition and at steady state. The flexible mathematical structure of C-STABILITY offers a promising foundation for exploring new mechanistic hypotheses and supporting the design of future experiments.

Pulp and paper mill sludges decrease soil erodibility

Declining carbon (C) content in agricultural soils threatens soil fertility and makes soil prone to erosion, which could be rectified with organic soil amendments. In a 4-yr field trial, we made a single application of three different organic sludges from the pulp and paper industry and studied their effects on cereal yield, soil C content, and fungal and bacterial composition. In laboratory rainfall simulations, we also studied the effects of the soil amendments on susceptibility to erosion and nutrient mobilization of a clay-textured soil by measuring the quality of percolation water passing through 40-cm intact soil monoliths during 2-d rainfall simulations over four consecutive years after application. A nutrient-poor fiber sludge reduced wheat yield in the first growing season, but there were no other significant effects on cereal yield or grain quality. An input of ∼8 Mg ha^-1 C with the soil amendments had only minor effects on soil C content after 4 yr, likely because of fast microbe-mediated turnover. The amendments clearly changed the fungal and bacterial community composition. All amendments significantly reduced suspended solids (SS) and total phosphorus (TP) concentrations in percolation water. The effect declined with time, but the reduction in SS and TP was still >25% 4 yr after application. We attributed the lower tendency for particle detachment in rain simulations to direct interactions of soil minerals with the added particulate organic matter and microbe-derived compounds that stabilize soil aggregates. In soils with low organic matter content, pulp and paper industry by-products can be a viable measure for erosion mitigation.

Effects of nitrogen addition on microbial residues and their contribution to soil organic carbon in China's forests from tropical to boreal zone

Atmospheric nitrogen (N) deposition has a significant influence on soil organic carbon (SOC) accumulation in forest ecosystems. Microbial residues, as by-products of microbial anabolism, account for a significant fraction of soil C pools. However, how N deposition affects the accumulation of soil microbial residues in different forest biomes remains unclear. Here, we investigated the effects of six/seven-year N additions on microbial residues (amino sugar biomarkers) in eight forests from tropical to boreal zone in eastern China. Our results showed a minor change in the soil microbial residue concentrations but a significant change in the contribution of microbial residue-C to SOC after N addition. The contribution of fungal residue-C to SOC decreased under low N addition (50 kg N ha^-1 yr^-1) in the tropical secondary forest (-19%), but increased under high N addition (100 kg N ha^-1 yr^-1) in the temperate Korean pine mixed forest (+21%). The contribution of bacterial residue-C to SOC increased under the high N addition in the subtropical Castanopsis carlesii forest (+26%) and under the low N addition in the temperate birch forest (+38%), respectively. The responses of microbial residue-C in SOC to N addition depended on the changes in soil total N concentration and fungi to bacteria ratio under N addition and climate. Taken together, these findings provide the experimental evidence that N addition diversely regulates the formation and composition of microbial-derived C in SOC in forest ecosystems.

Decline in the contribution of microbial residues to soil organic carbon along a subtropical elevation gradient

There has been an increasing interest in studying microbial necromasses and their contribution to soil organic carbon (SOC) accumulation. However, it remains unclear how the interaction among climate, plants, and soil influence the microbial anabolism and how microbial necromass contribute to SOC formation. Here, we assessed the relative contribution of microbial residues to SOC pool across a subtropical elevation gradient (ranged from 630 to 2130 m a.s.l.) representing a subtropical ecosystem on Wuyi Mountain in China, by using amino sugars as tracers. Analysis of topsoil (0-10 cm) amino sugars and the composition of microbial community across this gradient revealed that the soil total amino sugars accounting for 12.2-25.7% of the SOC pool, decreased with increasing elevation. Moreover, the linear reduction in the bacterial-derived carbon (C) and an increase in the ratio of fungal- to bacterial-derived C with increasing elevation suggested the reduction in the contribution of bacterial-derived C to SOC pool across this elevation gradient. The divergent changes in the contribution of the microbial residues to SOC infer a potential change in SOC composition and stability. The microbial-derived SOC formation and its climatic responses are influenced by the interaction of vegetation types and soil properties, with soil amorphous Fe being the determiner of soil amino sugar accrual. Our work highlights the importance of understanding ecosystem type and mineral composition in regulating microbial-mediated SOC formation and accumulation in responses to climate change in subtropical ecosystems.

Moderate over-feeding of different sources of metabolizable energy and protein improved gestational insulin resistance markers and maternal metabolic status of sheep around lambing

The objective of this study was to determine the effect of moderate over-nutrition of energy (using flaxseed as a source of n-3 fatty acids) and protein (using rumen-protected lysine and methionine) around parturition on prepartal insulin resistance (IR) and periparturient metabolic status and performance of ewes. For this purpose, 32 apparently healthy ewes (2.5 ± 1 years old, 42.19 ± 1.65 kg body weight (BW)) were randomly selected out of 200 pregnant Zell ewes on d 50 before the expected lambing. After receiving a ten-day adaptation diet, eight ewes were randomly allocated to one of the following four dietary treatments: 1) the adaptation diet that meets the metabolizable energy (ME) and protein (MP) requirements of ewes during late pregnancy as recommended by National Research Council = NRC (2007) (Control = CON). 2) A diet with 10% higher levels of ME than NRC (2007) recommendations using corn grain as a source of extra ME (HEC). 3) A diet with 10% higher levels of ME compared to NRC (2007) recommendations using flaxseed for additional ME (HEF). 4) A diet with a 10% higher level of MP than NRC (2007) recommendations using rumen-protected lysine and methionine as a source of extra MP (PRO). While the dietary treatments did not affect animals' dry matter intake (DMI), the CON ewes lost more BW starting from d 10 to d 30 relative to parturition compared to others (P < 0.05). Milk protein and fat yield (g/d) were significantly higher for PRO and HEF compared to HEC and CON ewes (P < 0.05). Moderately over-fed ewes with MP and ME had an improved insulin sensitivity (IS) compared to CON ones. The source of additional ME also impacted IR indices because HEC showed an enhancement in IS than HEF animals (P < 0.05). A lower IS in CON ewes was parallel with higher concentrations of plasma urea at prepartum (P < 0.01), lower levels of plasma cholesterol, triglyceride (P < 0.01) and glucose post-partum (P < 0.05), and a tendency for higher levels of beta-hydroxybutyrate (BHB) and non-esterified fatty acids (NEFA) in CON ewes during both pre- and post-partum periods. There were negative correlations between plasma urea, BHB, and NEFA with IR markers on d 7 prepartum in line with these results. Comparing data, we could not find a significant change in metabolic status among ewes fed with either PRO or HEF/HEC. In conclusion, the inclusion of 10% extra MP and ME could improve late gestation maternal IS and the metabolic status of dams around lambing.

Dynamics of microbial residues control the responses of mineral-associated soil organic carbon to N addition in two temperate forests

Numerous studies have investigated the impact of nitrogen (N) addition on ecosystem carbon (C) storage and cycling. However, how N addition regulates the dynamics of different soil organic carbon (SOC) fractions and the underlying microbial mechanisms remain unclear. In this study, we assessed microbial controls (through biomass, residues and enzymes) of different SOC fractions (particulate organic carbon, POC and mineral-associated organic carbon, MAOC) in response to six years of N addition (50 kg N ha^-1 yr^-1) in two temperate forests (Betula platyphylla vs. Quercus wutaishanica) in Northern China. Plant inputs (root biomass and leaf litterfall) and soil chemistry (pH, extractable inorganic N, and exchangeable cations) were unaltered by N addition in both forests. In the Q. wutaishanica forest, microbial biomass, residues, and enzymes were not sensitive to N addition, which may explain the lack of response in SOC and two fractions (POC and MAOC). However, in the B. platyphylla forest, although microbial biomass and enzymes as well as SOC and POC did not significantly change after N addition, both microbial residues (amino sugars) and MAOC significantly increased after N addition. Moreover, there was a strong positive correlation between microbial residues and MAOC pool within or across the two forests. Collectively, these results suggest that the dynamics of microbial residues play a crucial role in controlling the response of mineral-associated SOC to N addition in these two forests. Separating bulk soil into distinct functional pools and considering microbial residues should help reveal the nuanced response of soil C dynamics under N addition.

The legacy of trace metal deposition from historical anthropogenic river management: A regional driver of offshore sedimentary microbial diversity

River management, both modern and historical, have dramatically modified offshore environments. While numerous studies have described the modern impacts, very few have evaluated the legacies remaining from hundreds of years ago. Herein, we show trace metal enrichment in the surface sediment of the abandoned Yellow River Delta, hypothesized to be associated with ancient river management. Essentially, anthropogenic modification caused the river to shift, creating a 12.4×10³ km² area with elevated trace metals; characterized by clear metal deposition gradients. Geographical factors related to the ancient river mouth had the most significant influences on Zn (explained by distance to the river mouth, DTM) and Cd (DTM and sediment salinity), while the sediment absorptive capacity was associated with the reallocation of Cu (clay, silt, and iron), Ni (clay and iron), and Pb (silt and iron). Trace metal legacies showed stronger influences on prokaryotic diversity than on micro-eukaryotic diversity, with the former best described by changes in rare, rather than dominant families and classes, and explainable by an "overlapping micro-niche" model. The ancient river's legacies provide evidence of longer-term human disturbance over hundreds of years; as its impacts on associated benthic microbiomes have led to lessons for modern-day waterway management of benthic ecosystems.

The soil microbial carbon pump: From conceptual insights to empirical assessments

The global soil carbon (C) pool is massive, so relatively small changes in soil organic carbon (SOC) stocks can significantly alter atmospheric C and global climate. The recently proposed concept of the soil microbial carbon pump (MCP) emphasizes the active role of soil microbes in SOC storage by integrating the continual microbial transformation of organic C from labile to persistent anabolic forms. However, the concept has not been evaluated with data. Here, we combine datasets, including microbial necromass biomarker amino sugars and SOC, from two long-term agricultural field studies conducted by large United States bioenergy research programs. We interrogate the soil MCP concept by investigating the asynchronous responses of microbial necromass and SOC to land-use change. Microbial necromass appeared to preferentially accumulate in soil and be the dominant contributor to SOC accrual in diversified perennial bioenergy crops. Specifically, ~92% of the additional SOC enhanced by plant diversity was estimated to be microbial necromass C, and >76% of the additional SOC enhanced by land-use transition from annual to perennial crops was estimated to be microbial necromass. This suggests that the soil MCP was stimulated in diversified perennial agroecosystems. We further delineate and suggest two parameters-soil MCP capacity and efficacy-reflecting the conversion of plant C into microbial necromass and the contribution of microbial necromass to SOC, respectively, that should serve as valuable metrics for future studies evaluating SOC storage under alternative management in changing climates.

Microbial Community Analysis of Anaerobic Enrichment Cultures Supplemented with Bacterial Peptidoglycan as the Sole Substrate

Methanogenic microbial communities were enriched from rice paddy soil and anaerobic digester sludge using peptidoglycan purified from gram-negative Escherichia coli or gram-positive Micrococcus luteus as the sole substrate. Methane production data suggested the anaerobic degradation of peptidoglycan and also that peptidoglycan from E. coli had lower degradability. The community structures of enrichment cultures fed peptidoglycan from E. coli or M. luteus were similar, but distinctly different. A number of phylogenetically novel and uncultured bacteria, particularly in the phyla Bacteroidetes, WWE1, Armatimonadetes, and Verrucomicrobia, dominated the enrichment cultures, suggesting their involvement in anaerobic peptidoglycan degradation.

Metagenomic and 14 C tracing evidence for autotrophic microbial CO2 fixation in paddy soils

Autotrophic carbon dioxide (CO₂ ) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with ¹⁴ C-labelling to investigate all known autotrophic pathways and CO₂ assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%-82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of ¹⁴ C-CO₂ are assimilated into SOC (74.3-175.8 mg ¹⁴ C kg^-1 ) and microbial biomass (5.2-24.1 mg ¹⁴ C kg^-1 ) after 45 days incubation, where more than 70% of ¹⁴ C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.

Increasing the organic carbon stocks in mineral soils sequesters large amounts of phosphorus

Despite the fact that phosphorus (P) is critical for plant biomass production in many ecosystems, the implications of soil organic carbon (OC) sequestration for the P cycle have hardly been discussed yet. Thus, the aims of this study are, first, to synthesize results about the relationship between C and P in soil organic matter (SOM) and organic matter inputs to soils, second, to review processes that affect the C:P ratio of SOM, and third, to discuss implications of OC storage in terrestrial ecosystems for P sequestration. The study shows that the storage of OC in mineral soils leads to the sequestration of large amounts of organic phosphorus (OP) since SOM in mineral soils is very rich in P. The reasons for the strong enrichment of OP with respect to OC in soils are the mineralization of OC and the formation of microbial necromass that is P-rich as well as the strong sorption of OP to mineral surfaces that prevents OP mineralization. In particular, the formation of mineral-associated SOM that is favorable for storing OC in soil over decadal to centennial timescales sequesters large amounts of OP. Storage of 1,000 kg C in the clay size fraction in the topsoils of croplands sequesters 13.1 kg P. In contrast, the OC:OP ratios of wood and of peatlands are much larger than the ones in cropland soils. Thus, storage of C in wood in peatlands sequesters much less P than the storage of OC in mineral soils. In order to increase the C stocks in terrestrial ecosystems and to lock up as little P as possible, it would be more reasonable to protect and restore peatlands and to produce and preserve wood than to store OC in mineral soils.

Connections and Feedback: Aquatic, Plant, and Soil Microbiomes in Heterogeneous and Changing Environments

Plant, soil, and aquatic microbiomes interact, but scientists often study them independently. Integrating knowledge across these traditionally separate subdisciplines will generate better understanding of microbial ecological properties. Interactions among plant, soil, and aquatic microbiomes, as well as anthropogenic factors, influence important ecosystem processes, including greenhouse gas fluxes, crop production, nonnative species control, and nutrient flux from terrestrial to aquatic habitats. Terrestrial microbiomes influence nutrient retention and particle movement, thereby influencing the composition and functioning of aquatic microbiomes, which, themselves, govern water quality, and the potential for harmful algal blooms. Understanding how microbiomes drive links among terrestrial (plant and soil) and aquatic habitats will inform management decisions influencing ecosystem services. In the present article, we synthesize knowledge of microbiomes from traditionally disparate fields and how they mediate connections across physically separated systems. We identify knowledge gaps currently limiting our abilities to actualize microbiome management approaches for addressing environmental problems and optimize ecosystem services.

Soil carbon loss with warming: New evidence from carbon-degrading enzymes

Climate warming affects soil carbon (C) dynamics, with possible serious consequences for soil C stocks and atmospheric CO2 concentrations. However, the mechanisms underlying changes in soil C storage are not well understood, hampering long-term predictions of climate C-feedbacks. The activity of the extracellular enzymes ligninase and cellulase can be used to track changes in the predominant C sources of soil microbes and can thus provide mechanistic insights into soil C loss pathways. Here we show, using meta-analysis, that reductions in soil C stocks with warming are associated with increased ratios of ligninase to cellulase activity. Furthermore, whereas long-term (≥5 years) warming reduced the soil recalcitrant C pool by 14%, short-term warming had no significant effect. Together, these results suggest that warming stimulates microbial utilization of recalcitrant C pools, possibly exacerbating long-term climate-C feedbacks.

Dark microbial CO2 fixation in temperate forest soils increases with CO2 concentration

Dark, that is, nonphototrophic, microbial CO₂ fixation occurs in a large range of soils. However, it is still not known whether dark microbial CO₂ fixation substantially contributes to the C balance of soils and what factors control this process. Therefore, the objective of this study was to quantitate dark microbial CO₂ fixation in temperate forest soils, to determine the relationship between the soil CO₂ concentration and dark microbial CO₂ fixation, and to estimate the relative contribution of different microbial groups to dark CO₂ fixation. For this purpose, we conducted a ¹³ C-CO₂ labeling experiment. We found that the rates of dark microbial CO₂ fixation were positively correlated with the CO₂ concentration in all soils. Dark microbial CO₂ fixation amounted to up to 320 µg C kg^-1  soil day^-1 in the Ah horizon. The fixation rates were 2.8-8.9 times higher in the Ah horizon than in the Bw1 horizon. Although the rates of dark microbial fixation were small compared to the respiration rate (1.2%-3.9% of the respiration rate), our findings suggest that organic matter formed by microorganisms from CO₂ contributes to the soil organic matter pool, especially given that microbial detritus is more stable in soil than plant detritus. Phospholipid fatty acid analyses indicated that CO₂ was mostly fixed by gram-positive bacteria, and not by fungi. In conclusion, our study shows that the dark microbial CO₂ fixation rate in temperate forest soils increases in periods of high CO₂ concentrations, that dark microbial CO₂ fixation is mostly accomplished by gram-positive bacteria, and that dark microbial CO₂ fixation contributes to the formation of soil organic matter.