Microbial Decomposers Research Articles

Seasonal effects on the stoichiometry of microbes, primary production, and nutrient cycling

We develop a compartment model inspired by producer–herbivore–microbe soil food webs and determine how the naturally occurring seasonal variation in producer and detrital quality affects microbial nutrient cycling and the feedback to primary production. We show that seasonal changes in the stoichiometric quality of the producer coupled with the efficiency of herbivore grazing could induce a switch in the stoichiometric signature and therefore the functioning of the microbial community. Microbial decomposers are responsible for the flux of essential nutrients through an ecosystem. Our model enables one to quantitatively understand the tipping points between bacterially or fungally dominated decomposer communities, and more generally, the complex relationships between microbial decomposers, primary production, and nutrient cycling.

Mixture effects of a fungicide and an antibiotic: Assessment and prediction using a decomposer-detritivore system

Antimicrobials, such as fungicides and antibiotics, pose a risk for microbial decomposers (i.e., bacteria and aquatic fungi) and invertebrate detritivores (i.e., shredders) that play a pivotal role in the ecosystem function of leaf litter breakdown. Although waterborne toxicity and diet-related effects (i.e., dietary exposure and microorganism-mediated alterations in food quality for shredders) of fungicides and antibiotics on decomposer-detritivore systems have been increasingly documented, their joint effect is unknown. We therefore assessed waterborne and dietary effects of an antimicrobial mixture consisting of the fungicide azoxystrobin (AZO) and the antibiotic ciprofloxacin (CIP) on microbial decomposers and the shredder Gammarus fossarum using a tiered approach. We compared effect sizes measured in the present study with model predictions (i.e., independent action) based on published data. During a 7-day feeding activity assay quantifying waterborne toxicity in G. fossarum, the leaf consumption of gammarids was reduced by ∼60 % compared to the control when subjected to the mixture at concentrations of each component causing a 20 % reduction in the same response variable when applied individually. Moreover, the selective feeding of gammarids during the food choice assay indicated alterations in food quality induced by the antimicrobial mixture. The food selection and, in addition, the decrease in microbial leaf decomposition is likely linked to changes in leaf-associated bacteria and fungi. During a long-term assay, energy processing, growth and energy reserves of gammarids were increased in presence of 15 and 500 μg/L of AZO and CIP, respectively, through the dietary pathway. These physiological responses were probably driven by CIP-induced alterations in the gut microbiome or immune system of gammarids. In general, model predictions matched observed effects caused by waterborne exposure on the leaf consumption, energy processing and growth of gammarids during short- and long-term assays, respectively. However, when complex horizontal (bacteria and aquatic fungi) and vertical (leaf-associated microorganisms and shredders) interactions were involved, model predictions partly over- or underestimated mixture effects. Therefore, the present study identifies uncertainties of mixture effect predictions for complex biological systems calling for studies targeting the underlying processes and mechanisms.

Comparative Decomposition of Humans and Pigs: Soil Biogeochemistry, Microbial Activity and Metabolomic Profiles.

Vertebrate decomposition processes have important ecological implications and, in the case of human decomposition, forensic applications. Animals, especially domestic pigs (Sus scrofa), are frequently used as human analogs in forensic decomposition studies. However, recent research shows that humans and pigs do not necessarily decompose in the same manner, with differences in decomposition rates, patterns, and scavenging. The objective of our study was to extend these observations and determine if human and pig decomposition in terrestrial settings have different local impacts on soil biogeochemistry and microbial activity. In two seasonal trials (summer and winter), we simultaneously placed replicate human donors and pig carcasses on the soil surface and allowed them to decompose. In both human and pig decomposition-impacted soils, we observed elevated microbial respiration, protease activity, and ammonium, indicative of enhanced microbial ammonification and limited nitrification in soil during soft tissue decomposition. Soil respiration was comparable between summer and winter, indicating similar microbial activity; however, the magnitude of the pulse of decomposition products was greater in the summer. Using untargeted metabolomics and lipidomics approaches, we identified 38 metabolites and 54 lipids that were elevated in both human and pig decomposition-impacted soils. The most frequently detected metabolites were anthranilate, creatine, 5-hydroxyindoleacetic acid, taurine, xanthine, N-acetylglutamine, acetyllysine, and sedoheptulose 1/7-phosphate; the most frequently detected lipids were phosphatidylethanolamine and monogalactosyldiacylglycerol. Decomposition soils were also significantly enriched in metabolites belonging to amino acid metabolic pathways and the TCA cycle. Comparing humans and pigs, we noted several differences in soil biogeochemical responses. Soils under humans decreased in pH as decomposition progressed, while under pigs, soil pH increased. Additionally, under pigs we observed significantly higher ammonium and protease activities compared to humans. We identified several metabolites that were elevated in human decomposition soil compared to pig decomposition soil, including 2-oxo-4-methylthiobutanoate, sn-glycerol 3-phosphate, and tryptophan, suggesting different decomposition chemistries and timing between the two species. Together, our work shows that human and pig decomposition differ in terms of their impacts on soil biogeochemistry and microbial decomposer activities, adding to our understanding of decomposition ecology and informing the use of non-human models in forensic research.

Can photocatalytic and magnetic nanoparticles be a threat to aquatic detrital food webs?

Freshwaters are likely to serve as reservoirs for engineered nanomaterials (ENMs) due to their accelerated unintentional release, increasing the relevance of assessing their impacts on aquatic biota and the ecosystem processes they drive. Stream-dwelling microbes, particularly fungi, and invertebrate shredders play an essential role in the decomposition of organic matter and transfer of energy to higher trophic levels. We assessed the impacts of two photocatalytic (nano-TiO2 and erbium doped nano-TiO2) and one magnetic (nano-CoFe2O4) ENMs on detrital-based food webs in freshwaters by exposing chestnut leaves, colonized by stream-dwelling microbes, to a series of concentrations (0.25–150 mg L−1) of these ENMs. Microbial decomposition and biomass of fungal communities, associated with leaves, were not affected by the ENMs. However, the activities of antioxidant enzymes of microbial decomposers were significantly (P < 0.05) stimulated by ENMs in a concentration-dependent way, suggesting oxidative stress in stream microbial communities. The stronger responses of these stress biomarkers against nano-TiO2 (increase upto 837.5% for catalase, 1546.8% for glutathione peroxidase and 1154.6% for glutathione S-transferase) suggest a higher toxicity of this ENM comparing to the others. To determine whether the effects could be transferred across trophic levels, the invertebrate shredder Sericostoma sp. was exposed to ENMs (1 and 50 mg L−1) for 5 days either via contaminated water or contaminated food (leaf litter). Leaf consumption rate by shredders decreased significantly (P < 0.05) with increasing concentrations of ENMs via food or water; the effects were more pronounced when exposure occurred via contaminated food (up to 99.3%, 90.7% and 90.3% inhibition by nano-Er:TiO2, nano-CoFe2O4 and nano-TiO2, respectively). Overall, the tested photocatalytic and magnetic ENMs can be harmful to microbial decomposers and invertebrate shredders further compromising detrital-based food webs in streams.

Gene analysis reveals that leaf litter from Epichloë endophyte-infected perennial ryegrass alters diversity and abundance of soil microbes involved in nitrification and denitrification

Although Epichloë endophytes are present only in aboveground tissues of grasses they indirectly influence soil biological characteristics through increased litter incorporation and root exudation. Epichloë endophytes have been reported to affect the decomposition rates of litter by altering litter quality and microbial decomposers to affect soil characteristics. However, it is not well-studied that underlying effects on functional genes involved in nitrification and denitrification after incorporation of litter containing Epichloë endophytes into soil. We collected soil samples at S0 (first litter incorporation), S1 (second litter incorporation), S2 (third litter incorporation) and S3 (120 days after the third litter incorporation) times after incorporation of litter that was either infected with the fungal endophyte Epichloë festucae var. Lolii or free of Epichloë endophyte, respectively. . We sampled the soil fororganic carbon (OC), total nitrogen (TN), total phosphorus (TP), ammonium nitrogen (NH4+-N: AN), nitrate nitrogen (NO3−-N: NN), soil microbial biomass carbon (MBC), nitrogen (MBN), ammonia-oxidizing bacteria (AOB-amoA) and ammonia-oxidizing archaea (AOA-amoA) functional genes for nitrification, nitrite reduction (nirS and nirK) and nitrous oxide reduction (nosZ) functional genes for denitrification. We found that Epichloë-infected plant increased the soil properties (OC, TN, AN, NN) and microbial biomass C in S1 to S3 times, and microbial biomass N in S2 and S3 times, but reduced soil pH in S1 times and the C_N ratio in S2 and S3 times by litter incorporation. The absolute abundance of the AOB-amoA functional gene at S1 and S3 times and relative abundances of Planctomycetes, Methylobacterium, Nitosomonas, Gemmata, Geodermatophilus and Sinorhizobium in the nirK functional gene community were significantly higher in soil with Epichloë-infected litter compared to soil with Epichloë-free litter at S1 and S3 times. While the absolute abundance at S1 and S3 times and diversity at S3 times of the nirK functional gene, and the absolute abundance at S1 to S3 times and diversity at S1 times of the nosZ functional gene, and relative abundance of Proteobacteria in the AOB-amoA functional gene were significantly lower in soil with litter containing Epichloë endophyte than that of soil with litter without the endophyte. The soil moisture, and the contents of TP, OC, AN and MBN were the best explanatory variables for the altered microbial community. Our results provide a new understanding of the responses of soil nitrification and denitrification genes through incorporation of litter containing Epichloë endophytes into soil.

Impact of long-term fertilizer and summer warming treatments on bulk soil and birch rhizosphere microbial communities in mesic arctic tundra

ABSTRACT Recent climate warming in the Arctic is enhancing microbial decomposition of soil organic matter, which may result in globally significant greenhouse gas releases to the atmosphere. To better predict future impacts, bacterial and fungal community structures in both the bulk soil and the rhizosphere of Arctic birch, Betula glandulosa, were determined in control, greenhouse summer warming, and annual factorial nitrogen (N) and phosphate (P) addition treatments twelve years after their establishment. DNA sequence analyses at multiple taxonomic levels consistently indicated substantial bulk soil and rhizosphere microbial community differences among the fertilization treatments but no significant greenhouse effects. These results suggest that climate warming will likely increase the activity rates of soil microbial decomposers but without substantially altering the structure of either the bacterial or fungal communities. Differential abundance testing revealed changes in ectomycorrhizal fungal species of the genus Thelephora in both bulk soil and rhizosphere, with increases in their relative abundance in P and N + P amended plots compared with warming and controls. Because birch is the principal low Arctic ectomycorrhizal host, our results suggest that these fungi may promote this shrub’s competitiveness where tundra soil nutrient availability is enhanced by warming or other means, ultimately contributing to arctic vegetation “greening.”

Chemical composition of soil organic carbon from mixed aspen‐conifer forests characterized with Fourier transform infrared spectroscopy

AbstractForest species control the quantity and chemistry of organic matter input, which in interaction with the soil physicochemical properties, environmental conditions and microbial community associated with a given ecosystem may result in specific patterns of soil organic carbon (SOC) stabilization and chemistry. The objectives of this study were: (a) to characterize the chemistry of soil organic matter and SOC fractions across the gradient from pure aspen (Populus tremuloidesMichx.) to pure conifer (Abies lasiocarpa(Hook.) Nutt. andPseudotsuga menziesii(Mirbel) Franco) stands in semi‐arid montane forests, and (b) to determine whether the effect of overstory composition on SOC chemistry was patent beyond the influence of site conditions and microbial decomposer community. We used Fourier transform infrared spectroscopy to analyse the chemistry of bulk soil (BS), light fraction (LF) and mineral‐associated SOC (MoM) from mineral soils (0–15 cm) sampled across the natural gradient of aspen and mixed conifer stands from northern and southern Utah. Vegetation overstory had a subtle effect on the MoM fraction, indicating higher proportion of aliphatic C with aspen dominance, whereas there were no differences in LF chemistry between vegetation types. Independently of the vegetation cover type, the MoM fraction was enriched in aliphatic C compared to the LF, although the proportion of polysaccharides and C‐O groups increased in the MoM fraction for plot samples. Differentiation between spectra from soils developed on sedimentary rock and soils developed on basalt, quartzite and limestone, highlighted the influence of parent material and mineralogy on MoM chemistry. The patterns in SOC fractions' chemistry do not allow an affirmation that greater SOC storage under aspen is due to the accumulation of recalcitrant compounds (i.e., aliphatic C) and controlled by litter chemistry. Rather, they suggest that the ensemble of litter chemistry, microbial community and soil properties in aspen stands enhances SOC storage.HighlightsVegetation overstory and site characteristics (e.g., parent material) influence SOC chemistry and stabilization patterns.Light fraction SOC spectra did not differ between forest species in the aspen‐conifer ecotone.The proportion of aliphatic C in mineral‐associated organic carbon (MoM) increased with aspen dominance.The effect of overstory composition on MoM chemistry was patent beyond the influence of site conditions and microbial decomposer community.

Monitoring organic-matter decomposition and environmental drivers in restored vernal pools

Vernal pools are small, shallow and ephemeral freshwater wetlands, often located in forests. Despite harboring high levels of biodiversity and being biochemical hotspots, they have been severely degraded by human activities. Restoration of vernal pools has become a priority for resource managers, and monitoring of restoration projects is needed to track the effectiveness of restoration techniques. In this study, we analyzed the ecological functioning of natural and restored vernal pools in the forest of Chinon (France) four years after a restoration project. Specific aims were to: (1) compare organic-matter decomposition rates between natural and restored pools, and (2) evaluate the main drivers of organic-matter decomposition in these two types of pool. In five natural and nine restored vernal pools, a standardized organic-matter decomposition assay (cotton strip) was deployed for up to 57 days. Each pool was characterised in terms of vegetation type, water and soil quality. We found that decomposition rates did not differ between natural and restored pools. The natural pools, however, had the greater stores of total organic carbon (TOC) content, and Sphagnum moss cover. Across both pool types, decomposition rates were positively associated with canopy openness and vascular plant cover, suggesting a possible ‘priming effect’ of primary producers on microbial decomposers. Sphagnum moss cover and some soil variables, such as TOC, were associated with slowed decomposition, highlighting the potential of Sphagnum spp. at influencing microbial activity. We suggest that future studies couple the cotton strip assay with biotic indices to assess the overall functioning of these wetlands.

Effects of sulfonamide antibiotics on aquatic microbial community composition and functions

Knowledge on interactions among microbial communities colonizing various streambed substrata (e.g. cobbles, sediment, leaf-litter etc.) is essential when investigating the functioning of stream ecosystems. However, these interactions are often forgotten when assessing the responses of aquatic microbial communities to chemical contamination. Using a stream microcosm approach, the respective impact of two sulfonamide antibiotics (sulfamethoxazole and sulfamethazine) on the ability of microbial heterotrophs to decompose alder leaves was investigated in the presence or absence of periphyton. Our hypothesis suggested that sulfonamides would negatively impair microbial litter decomposition and that periphyton could possibly alleviate this effect by stimulating microbial decomposer activity through a priming effect. Results showed that the presence of periphyton enriched water with oxygen and labile dissolved organic carbon forms. However, these labile organic carbon sources did not stimulate leaf-litter decomposition but mostly decoupled microbial decomposer activity from particulate organic matter to dissolved organic matter through negative priming. Also, the two sulfonamide molecules did not affect the leaf-litter decomposition process but significantly decreased bacterial biomass accrual on leaves. The reduction of bacteria was concomitant with an increase in biomass-specific β-glucosidase activity and this was attributed to a stress response from bacteria to sulfonamides. Further research looking at microbial interactions would provide for better assessment of chemical contamination effects in communities and processes in stream ecosystems.

From pools to flow: The PROMISE framework for new insights on soil carbon cycling in a changing world

Soils represent the largest terrestrial reservoir of organic carbon, and the balance between soil organic carbon (SOC) formation and loss will drive powerful carbon-climate feedbacks over the coming century. To date, efforts to predict SOC dynamics have rested on pool-based models, which assume classes of SOC with internally homogenous physicochemical properties. However, emerging evidence suggests that soil carbon turnover is not dominantly controlled by the chemistry of carbon inputs, but rather by restrictions on microbial access to organic matter in the spatially heterogeneous soil environment. The dynamic processes that control the physicochemical protection of carbon translate poorly to pool-based SOC models; as a result, we are challenged to mechanistically predict how environmental change will impact movement of carbon between soils and the atmosphere. Here, we propose a novel conceptual framework to explore controls on belowground carbon cycling: Probabilistic Representation of Organic Matter Interactions within the Soil Environment (PROMISE). In contrast to traditional model frameworks, PROMISE does not attempt to define carbon pools united by common thermodynamic or functional attributes. Rather, the PROMISE concept considers how SOC cycling rates are governed by the stochastic processes that influence the proximity between microbial decomposers and organic matter, with emphasis on their physical location in the soil matrix. We illustrate the applications of this framework with a new biogeochemical simulation model that traces the fate of individual carbon atoms as they interact with their environment, undergoing biochemical transformations and moving through the soil pore space. We also discuss how the PROMISE framework reshapes dialogue around issues related to SOC management in a changing world. We intend the PROMISE framework to spur the development of new hypotheses, analytical tools, and model structures across disciplines that will illuminate mechanistic controls on the flow of carbon between plant, soil, and atmospheric pools.

Relative importance of soil microbes and litter quality on decomposition and nitrogen cycling in grasslands

AbstractMicrobial decomposers absorb nitrogen (N) to sustain growth during litter decomposition releasing surplus N into the soil. The balance between N release (mineralization) and absorption (immobilization) can alter nutrient cycling based mostly on the functional diversity in microbial communities. We examined the effects of soil microbes and litter quality on N cycling in an artificial grassland and two seminatural grasslands through a microcosm study. The artificial grassland soil had a higher respiration rate and a lower N mineralization rate, irrespective of the litter identity during incubation, when compared with the seminatural grassland soil. The release of mineralized nitrogen from litter was small for the artificial grassland because the soil microbes absorbed most of the mineralized N during decomposition. The artificial grassland soil had a low fungi:bacteria ratio (i.e., a high abundance of bacteria) and showed a clear separation of bacterial and fungal communities from the seminatural grassland soil. Our results suggested that stoichiometric constraint, not the biomass turnover rate, of microbial decomposers plays a key role in N cycling between aboveground and belowground communities in grasslands.

Contribution of fungal and invertebrate communities to wood decay in tropical terrestrial and aquatic habitats.

Wood is a major carbon input into aquatic ecosystems and is thought to decay slowly, yet surprisingly little terrestrial carbon accumulates in marine sediments. A better mechanistic understanding of how habitat conditions and decomposer communities influence wood decay processes along the river-estuary-ocean continuum can address this seeming paradox. We measured mass loss, wood element, and polymer concentrations, quantified invertebrate-induced decay, and sequenced fungal communities associated with replicate sections of Guazuma branch wood submerged in freshwater, estuarine, and near-shore marine habitats and placed on the soil surface in nearby terrestrial habitats in three watersheds in the tropical eastern Pacific. Over 15months, we found that wood decayed at similar rates in estuarine, marine, and terrestrial sites, reflecting the combined activity of invertebrate and microbial decomposers. In contrast, in the absence of shipworms (Teredinidae), which accounted for ~40% of wood mass loss in the estuarine habitats, decay proceeded more slowly in freshwater. Over the experiment, wood element chemistry diverged among freshwater, estuarine, and marine habitats, due to differences in both nutrient losses (e.g., potassium and phosphorus) and gains (e.g., calcium and aluminum) through decay. Similarly, we observed changes in wood polymer content, with the highest losses of cellulose, hemicellulose, and lignin moieties in the marine habitat. Aquatic fungal communities were strongly dominated by ascomycetes (88-99% of taxa), compared to terrestrial communities (55% ascomycetes). Large differences in fungal diversity were also observed across habitats with threefold higher richness in terrestrial than freshwater habitats and twofold higher diversity in freshwater than estuarine/marine habitats. Divergent decay trajectories across habitats were associated with widespread order-level differences in fungal composition, with distinct communities found in freshwater, estuarine and marine habitats. However, few individual taxa that were significantly associated with mass loss were broadly distributed, suggesting a high level of functional redundancy. The rapid processing of wood entering tropical rivers by microbes and invertebrates, comparable to that on land, indicates that estuaries and coastal oceans are hotspots not just for the processing of particulate and dissolved organic carbon, but also for woody debris and for the breakdown of lignin, the most recalcitrant polymer in plant tissue.

Responses of active soil microorganisms facing to a soil biostimulant input compared to plant legacy effects

Agriculture is changing to rely on agroecological practices that take into account biodiversity, and the ecological processes occurring in soils. The use of agricultural biostimulants has emerged as a valid alternative to chemicals to indirectly sustain plant growth and productivity. Certain BS have been shown to select and stimulate plant beneficial soil microorganisms. However, there is a lack of knowledge on the effects and way of action of the biostimulants operating on soil functioning as well as on the extent and dynamic of these effects. In this study we aimed to decipher the way of action of a seaweed and amino-acids based biostimulant intended to be applied on soil crop residues to increase their microbial mineralization and the further release of nutrients. By setting-up a two-phase experiment (soil plant-growing and soil incubation), our objectives were to (1) determine the effects of the soil biostimulant over time on the active soil bacteria and fungi and the consequences on the organic carbon mineralization in bare soils, and (2) assess the biostimulant effects on soil microorganisms relatively to plant legacy effects in planted soils. We demonstrated that the soil biostimulant had a delayed effect on the active soil microorganisms and activated both plant growth promoting bacteria and saprophytes microorganisms at the medium-term of 49 days. However, the changes in the abundances of active microbial decomposers were not associated to a higher mineralization rate of organic carbon derived from soil and/or litter. The present study assessed the biostimulant beneficial effect on active soil microbial communities as similar as or even higher than the legacy effects of either A. thaliana or T. aestivum plants. We specifically showed that the biostimulant increased the active fungal richness to a higher extent than observed in soils that previously grew the two plants tested.

Soil Microbial Community and Litter Quality Controls on Decomposition Across a Tropical Forest Disturbance Gradient

Industrial logging and agricultural expansion are driving rapid transformations of tropical ecosystems, modifying patterns in above-ground plant and below-ground microbial communities. However, the extent to which these changes in biodiversity drive modifications of ecosystem process rates such as leaf litter decomposition is poorly understood. To determine the relative effects of changes to the chemical quality of litter and shifts in microbial decomposers on leaf litter decomposition rates, we performed a controlled, reciprocal transplant, litter decomposition experiment across a tropical land-use disturbance gradient. Litter mixtures and soils were collected from old growth forest, moderately logged forest, heavily logged forest, and oil palm plantation in Sabah, Malaysia, and combined in a fully crossed, factorial microcosm experiment maintained under controlled environmental conditions. We found that whilst litter quality was the most important predictor of litter mass loss, soil origin was also significant, explaining between 5.17 and 15.43% of total variation. Microbial decomposer communities from old growth forest had greater functional breadth relative to those from logged forests and oil palm plantation as all litter types decomposed faster when combined with old growth soil. The most chemically recalcitrant litter (lowest N, highest lignin, lignin:N, and C:N ratio) from moderate logged forest decomposed faster when combined with its “home” soil (Home-Field Advantage) whilst the most labile litter from oil palm decomposed slowest when combined with its “home” soil. This was correlated with lower total soil microbial biomass. Taken together, these findings demonstrate that whilst litter quality regulated rates of litter decomposition across the disturbance gradient, soil microbial decomposer communities were functionally dissimilar between land uses and explained a significant proportion of variation. The impact of disturbance on soil, including microbial community structure, should be considered alongside changes to plant communities when assessing effects on crucial ecosystem processes such as decomposition.

Invasion of Native Riparian Forests by Acacia Species Affects In-Stream Litter Decomposition and Associated Microbial Decomposers.

The invasion of native riparian forests by exotic tree species can lead to profound changes in the ecological integrity of freshwater ecosystems. We assessed litter decomposition of native (Alnus glutinosa and Quercus robur) and invasive (Acacia melanoxylon and Acacia dealbata) tree species, and associated microbial activity and community structure, after being immersed for conditioning in 3 reference and 3 "invaded" streams in Serra da Lousã (central Portugal) and used in microcosms simulating stream conditions. Litter decomposition differed among species, in the order: Al. glutinosa > Q. robur > (Ac. melanoxylon ~ Ac. dealbata). Alnus glutinosa litter decomposed faster probably because it was soft and had high nitrogen concentration for decomposers. Quercus robur litter decomposed slower most likely because it was tough and had high polyphenol and low nitrogen concentrations. Acacia melanoxylon litter was the toughest and had a thick cuticle that likely acted as a physical barrier for microbial colonization. In Ac. dealbata, the small-sized leaflets and high lignin concentration may have limited microbial litter decomposition. Litter decomposition was faster in "invaded" streams, probably because they were N-limited and increases in nitrogen concentration in water, promoted by Acacia species invasion, stimulated microbial activity on litter. The aquatic hyphomycete community structure differed among litter species and between stream types, further suggesting that microbes were sensitive to litter characteristics and water nutrient concentrations. Overall, the invasion of native riparian forests by Acacia species may affect microbial decomposer activity, thus altering important stream ecosystem processes, such as litter decomposition and nutrient cycles.

Biodiversity mediates the effects of stressors but not nutrients on litter decomposition.

Understanding the consequences of ongoing biodiversity changes for ecosystems is a pressing challenge. Controlled biodiversity-ecosystem function experiments with random biodiversity loss scenarios have demonstrated that more diverse communities usually provide higher levels of ecosystem functioning. However, it is not clear if these results predict the ecosystem consequences of environmental changes that cause non-random alterations in biodiversity and community composition. We synthesized 69 independent studies reporting 660 observations of the impacts of two pervasive drivers of global change (chemical stressors and nutrient enrichment) on animal and microbial decomposer diversity and litter decomposition. Using meta-analysis and structural equation modeling, we show that declines in decomposer diversity and abundance explain reduced litter decomposition in response to stressors but not to nutrients. While chemical stressors generally reduced biodiversity and ecosystem functioning, detrimental effects of nutrients occurred only at high levels of nutrient inputs. Thus, more intense environmental change does not always result in stronger responses, illustrating the complexity of ecosystem consequences of biodiversity change. Overall, these findings provide strong evidence that the consequences of observed biodiversity change for ecosystems depend on the kind of environmental change, and are especially significant when human activities decrease biodiversity.

Nitrogen effects on quantity, chemistry, and decomposability of Pinus densiflora and Quercus variabilis litters under elevated CO2 and warming

The effects of increased nitrogen (N) availability through atmospheric deposition on the quantity and quality of tree leaf litter have been widely reported. However, such N effects under co-elevated CO2 concentration ([CO2]) and air temperature (Tair) have not been investigated. In this study, changes in biomass and chemistry of litter of Pinus densiflora S. et Z. (pine) and Quercus variabilis Blume (oak) saplings with two levels of each N × [CO2] × Tair were investigated for two growing seasons. The levels of N, [CO2], and Tair were 2 and 6-fold of ambient N deposition, ambient and ambient + 285 ppmv, and ambient and ambient + 2.2 °C, respectively, on average across the two seasons. The concentrations of N, minerals, and carbon (C) compounds such as non-structural carbohydrate (NSC) and lignin as well as stoichiometry such as the ratio of C to N (C/N) and lignin to N (lignin/N) of litter were analyzed to determine litter chemistry. In addition, the legacy effect of changed chemistry on microbial decomposability of the litters were also assessed by measuring CO2 emission in a 60-day lab incubation experiment. The effect of high N addition on increasing litter production was consistent regardless of [CO2] and Tair for oak; however, for pine, N-induced increases in litter production were negated under elevated [CO2] and/or Tair, probably due to efficient uptake and use of N by pine under elevated [CO2] as well as lowered N demand via warming-induced stress under elevated Tair. High N-induced decreases in C/N and lignin/N was consistent across [CO2]-Tair combination for both species though other chemical components such as NSC and minerals including phosphorous, calcium, aluminum, and manganese varied inconsistently. The CO2 emission from the soils amended with litters of different chemistry was not correlated with litter chemistry, suggesting that changed litter chemistry under different N level × [CO2] × Tair may not affect litter decomposability in the soils. This study enlarges our understanding of the effect of increased N availability on litter quantity, chemical composition, and microbial decomposability under different [CO2] and Tair. However, a study with mature trees in a natural forest stand should further improve our understanding.

Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria

BackgroundIn a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed.ResultsThe β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling.ConclusionsOur findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated.DcAwnKbrAmVskAnqeJFRkXVideo

Biomass, chemical composition, and microbial decomposability of rice root and straw produced under co-elevated CO2 and temperature

Rice residue including root and straw are unique carbon (C) source in paddy soils. However, the potential changes in quantity and chemical composition of rice residue under co-elevated atmospheric CO2 concentration ([CO2]) and air temperature (Tair) and the legacy effect of the changed chemical composition on residue decomposition have not been investigated. This study was conducted to investigate biomass, chemical composition, and decomposability of rice root and straw produced under elevated [CO2] and Tair. Root and straw biomass increased by elevated [CO2] and elevated Tair, respectively, and the greatest biomass was achieved under co-elevated [CO2]-Tair for both root and straw. The concentration of lignin (recalcitrant) decreased while that of nonstructural carbohydrates (less recalcitrant) increased by co-elevated [CO2]-Tair. The ratio of lignin-to-nitrogen (lignin/N) decreased by co-elevated [CO2]-Tair compared to ambient [CO2]-Tair due to increased N and decreased lignin concentrations. Decomposability of root (lignin/N, 36.4) produced under co-elevated [CO2]-Tair was greater than that under ambient co-elevated [CO2]-Tair (lignin/N, 53.7); however, there was no difference in decomposability for straw, which had relatively narrow range of lignin/N (27.3–36.5) regardless of [CO2]-Tair conditions. The results of this study provide a novel insight into the changes in quantity and quality of rice residue under elevated [CO2]-Tair that are necessary to predict changes in paddy soil C sequestration under global warming.

Drought and plant litter chemistry alter microbial gene expression and metabolite production

Drought represents a significant stress to microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we lack a detailed understanding of the drought stress response of microbial decomposers. Here we present metatranscriptomic and metabolomic data on the physiological response of in situ microbial communities on plant litter to long-term drought in Californian grass and shrub ecosystems. We hypothesised that drought causes greater microbial allocation to stress tolerance relative to growth pathways. In grass litter, communities from the decade-long ambient and reduced precipitation treatments had distinct taxonomic and functional profiles. The most discernable physiological signatures of drought were production or uptake of compatible solutes to maintain cellular osmotic balance, and synthesis of capsular and extracellular polymeric substances as a mechanism to retain water. The results show a clear functional response to drought in grass litter communities with greater allocation to survival relative to growth that could affect decomposition under drought. In contrast, communities on chemically more diverse and complex shrub litter had smaller physiological differences in response to long-term drought but higher investment in resource acquisition traits across precipitation treatments, suggesting that the functional response to drought is constrained by substrate quality. Our findings suggest, for the first time in a field setting, a trade off between microbial drought stress tolerance, resource acquisition and growth traits in plant litter microbial communities.