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Soils contain immense diversity and support terrestrial ecosystem functions, but they face both anthropogenic and environmental stressors. While many studies have examined the influence of individual stressors on soils, how these perturbations will interact to shape soil communities and their ability to cycle nutrients is far less resolved. Here, we hypothesized that when soils experience multiple stressors their ability to maintain connected and stable communities is disrupted, leading to shifts in C and N pools. To test this, we maintained soils across three temperatures representative of seasonal variability (15, 20 and 30 °C) and introduced high or low doses of the common livestock antibiotic Monensin. We monitored respiration and examined changes to microbial communities through amplicon sequencing and network analyses. We also examined soil C and N pools to understand how temperature and antibiotics shape ecosystem function. We found that antibiotics and rising soil temperatures interacted to disrupt bacterial assemblages and network structure, allowing for a rise in fungal dominance and change in soil nutrient stoichiometry. Antibiotics alone decreased bacterial diversity, abundance, total extractable N, and microbial carbon use efficiency, while increasing bioavailable C. Higher temperatures independently homogenized fungal community composition, decreased dissolved organic C and increased soil respiration rates. These results emphasize that as soils encounter multiple stressors, ecosystem efficiency, stability and resilience may be diminished.
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... Fertilized embryos were semi-statically exposed to the solvent control (SC, 0.5% (v/v) DMSO) or BPAF (12.5 and 125 μg/L, representing an environmentally relevant concentration (Qiu et al., 2021;Song et al., 2012) and a higher exposure levels, respectively) in 96-well plates from 6 hpf to 7 dpf. The exposure concentrations of BPAF were the same as those in our previous study , and two exposure concentrations of chemicals were also set up in previous studies (Lucas et al., 2021;Qiu et al., 2021). There were three replicates per treatment and 60 embryos per replicate. ...
Bisphenol AF (BPAF) is an emerging contaminant prevalent in the environment as one of main substitutes of bisphenol A (BPA). It was found that BPAF exhibited estrogenic effects in zebrafish larvae in our previous study, while little is known about its effects on the thyroid and liver. A 7 d zebrafish embryotoxicity test was conducted to study the potential thyroid disruption and hepatotoxicity of BPAF. BPAF decreased levels of thyroid hormones and deiodinases but increased expressions of transthyretin at 12.5 and 125 µg/L after 7 d exposure, indicating that both the metabolism and transport of thyroid hormones were perturbed. The thyroid hormone receptor (TR) levels decreased significantly upon exposure to ≥12.5 µg/L BPAF, implying that BPAF acts as a TR antagonist, which coincided well with the prediction from the Direct Message Passing Neural Network. The liver impairment (mainly cell necrosis of hepatocytes) and apoptosis were triggered by 125 µg/L and ≥12.5 µg/L BPAF respectively, accompanied by the increased activities of caspase 3 and caspase 9. Thus BPAF might not be a safe alternative to BPA given the thyroid and liver toxicity. DMPNN appears useful to screen for thyroid disrupting activity from molecular structures.
Excessive use of antibiotics in the healthcare sector and livestock farming has amplified antimicrobial resistance (AMR) as a major environmental threat in recent years. Abiotic stresses, including soil salinity and water pollutants, can affect AMR in soils, which in turn reduces the yield and quality of agricultural products. The objective of this study was to investigate the effects of antibiotic resistance and abiotic stresses on antimicrobial resistance in agricultural soils. A systematic review of the peer-reviewed published literature showed that soil contaminants derived from organic and chemical fertilizers, heavy metals, hydrocarbons, and untreated sewage sludge can significantly develop AMR through increasing the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in agricultural soils. Among effective technologies developed to minimize AMR’s negative effects, salinity and heat were found to be more influential in lowering ARGs and subsequently AMR. Several strategies to mitigate AMR in agricultural soils and future directions for research on AMR have been discussed, including integrated control of antibiotic usage and primary sources of ARGs. Knowledge of the factors affecting AMR has the potential to develop effective policies and technologies to minimize its adverse impacts.
Increasing amounts of antibiotics are introduced into soils, raising great concerns on their ecotoxicological impacts on the soil environment. This work investigated the individual and joint toxicity of three antibiotics, tetracycline (TC), sulfonamide (SD) and erythromycin (EM) via a whole-cell bioreporter assay. TC, SD and EM in aqueous solution demonstrated cytotoxicity, whilst soil exposure showed genotoxicity, indicating that soil particles possibly affected the bioavailability of antibiotics. Toxicity of soils exposed to TC, SD and EM changed over time, demonstrating cytotoxic effects within 14-d exposure and genotoxic effects after 30 days. Joint toxicity of TC, SD and EM in soils instead showed cytotoxicity, suggesting a synergetic effect. High-throughput sequencing suggested that the soil microbial response to individual antibiotics and their mixtures showed a different pattern. Soil microbial community composition was more sensitive to TC, in which the abundance of Pseudomonas, Pirellula, Subdivision3_genera_incertae_sedis and Gemmata varied significantly. Microbial community functions were significantly shifted by EM amendments, including signal transduction mechanisms, cytoskeleton, cell wall/membrane/envelope biogenesis, transcription, chromatin structure and dynamics, and carbohydrate transport and metabolism. This work contributes to a better understanding of the ecological effects and potential risks of individual and joint antibiotics on the soil environment.
Environmental stress is increasing worldwide, yet we lack a clear picture of how stress disrupts the stability of microbial communities and the ecosystem services they provide. Here, we present the first evidence that naturally-occurring microbiomes display network properties characteristic of unstable communities when under persistent stress. By assessing changes in diversity and structure of soil microbiomes along 40 replicate stress gradients (elevation/water availability gradients) in the Florida scrub ecosystem, we show that: (1) prokaryotic and fungal diversity decline in high stress, and (2) two network properties of stable microbial communities—modularity and negative:positive cohesion—have a clear negative relationship with environmental stress, explaining 51–78% of their variation. Interestingly, pathogenic taxa/functional guilds decreased in relative abundance along the stress gradient, while oligotrophs and mutualists increased, suggesting that the shift in negative:positive cohesion could result from decreasing negative:positive biotic interactions consistent with the predictions of the Stress Gradient Hypothesis. Given the crucial role microbiomes play in ecosystem functions, our results suggest that, by limiting the compartmentalization of microbial associations and creating communities dominated by positive associations, increasing stress in the Anthropocene could destabilize microbiomes and undermine their ecosystem services.
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem, including chemical-literature links from Thieme Chemistry, chemical and physical property links from SpringerMaterials, and patent links from the World Intellectual Properties Organization (WIPO). PubChem's homepage and individual record pages were updated to help users find desired information faster. This update involved a data model change for the data objects used by these pages as well as by programmatic users. Several new services were introduced, including the PubChem Periodic Table and Element pages, Pathway pages, and Knowledge panels. Additionally, in response to the coronavirus disease 2019 (COVID-19) outbreak, PubChem created a special data collection that contains PubChem data related to COVID-19 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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.
Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse‐chase. Exposure to manure from antibiotic‐treated cattle caused: (i) changes in microbial community structure; and (ii) alterations in elemental cycling throughout the terrestrial system. This exposure caused changes in fungal : bacterial ratios, as well as changes in bacterial community structure. Additionally, exposure to manure from cattle treated with pirlimycin resulted in an approximate two‐fold increase in ecosystem respiration of recently fixed‐carbon, and a greater proportion of recently added nitrogen in plant and soil pools compared to the control manure. Manure from antibiotic‐treated cattle therefore affects terrestrial ecosystem function via the soil microbiome, causing decreased ecosystem carbon use efficiency, and altered nitrogen cycling.
Bacteria and fungi secrete antibiotics to suppress and kill other microbes, but can these compounds be agents of competition against macroorganisms? We explore how one competitive tactic, antibiotic production, can structure the composition and function of brown food webs. This aspect of warfare between microbes and invertebrates is particularly important today as antibiotics are introduced into ecosystems via anthropogenic activities, but the ecological implications of these introductions are largely unknown. We hypothesized that antimicrobial compounds act as agents of competition against invertebrate and microbial competitors. Using field-like mesocosms, we tested how antifungal and antibacterial compounds influence microbes, invertebrates, and decomposition in the brown food web. Both antibiotics changed prokaryotic microbial community composition, but only the antibacterial changed invertebrate composition. Antibacterials reduced the abundance of invertebrate detritivores by 34%. However, the addition of antimicrobials did not ramify up the food web as predator abundances were unaffected. Decomposition rates did not change. To test the mechanisms of antibiotic effects, we provided antibiotic-laden water to individual invertebrate detritivores in separate microcosm experiments. We found that the antibiotic compounds can directly harm invertebrate taxa, probably through a disruption of endosymbionts. Combined, our results show that antibiotic compounds could be an effective weapon for microbes to compete against both microbial and invertebrate competitors. In the context of human introductions, the detrimental effects of antibiotics on invertebrate communities indicates that the scope of this anthropogenic disturbance is much greater than previously expected.
Sphagnum‐dominated peatlands comprise a globally important pool of soil carbon (C) and are vulnerable to climate change. While peat mosses of the genus Sphagnum are known to harbor diverse microbial communities that mediate C and nitrogen (N) cycling in peatlands, the effects of climate change on Sphagnum microbiome composition and functioning are largely unknown. We investigated the impacts of experimental whole‐ecosystem warming on the Sphagnum moss microbiome, focusing on N2 fixing microorganisms (diazotrophs). To characterize the microbiome response to warming, we performed next‐generation sequencing of small subunit (SSU) rRNA and nitrogenase (nifH) gene amplicons and quantified rates of N2 fixation activity in Sphagnum fallax individuals sampled from experimental enclosures over two years in a northern Minnesota, USA bog. The taxonomic diversity of overall microbial communities and diazotroph communities, as well as N2 fixation rates, decreased with warming (P < 0.05). Following warming, diazotrophs shifted from a mixed community of Nostocales (Cyanobacteria) and Rhizobiales (Alphaproteobacteria) to predominance of Nostocales. Microbiome community composition differed between years, with some diazotroph populations persisting while others declined in relative abundance in warmed plots in the second year. Our results demonstrate that warming substantially alters the community composition, diversity, and N2 fixation activity of peat moss microbiomes, which may ultimately impact host fitness, ecosystem productivity, and C storage potential in peatlands.
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Sugarcane-soybean intercropping has been widely used to control disease and
improve nutrition in the field. However, the response of the soil microbial
community diversity and structure to intercropping is not well understood. Since
microbial diversity corresponds to soil quality and plant health, a pot experiment was
conducted with sugarcane intercropped with soybean. Rhizosphere soil was collected
40 days after sowing, and MiSeq sequencing was utilized to analyze the soil
microbial community diversity and composition. Soil columns were used to assess
the influence of intercropping on soil microbial activity (soil respiration and
carbon-use efficiency: nitrogen-use efficiency ratio). PICRUSt and FUNGuild
analysis were conducted to predict microbial functional profiling. Our results showed
that intercropping decreased pH by approximately 8.9% and enhanced the soil
organic carbon, dissolved organic carbon, and available nitrogen (N) by 5.5%, 13.4%,
and 10.0%, respectively. These changes in physicochemical properties corresponded
to increased microbial diversity and shifts in soil microbial communities.
Microbial community correlated significantly (p < 0.05) with soil respiration rates
and nutrient use efficiency. Furthermore, intercropping influenced microbial
functions, such as carbon fixation pathways in prokaryotes, citrate cycle (TCA cycle)
of bacteria and wood saprotrophs of fungi. These overrepresented functions might
accelerate nutrient conversion and control phytopathogens in soil.
Losses and gains in species diversity affect ecological stability1–7 and the sustainability of ecosystem functions and services8–13. Experiments and models have revealed positive, negative and no effects of diversity on individual components of stability, such as temporal variability, resistance and resilience2,3,6,11,12,14. How these stability components covary remains poorly understood¹⁵. Similarly, the effects of diversity on overall ecosystem stability¹⁶, which is conceptually akin to ecosystem multifunctionality17,18, remain unknown. Here we studied communities of aquatic ciliates to understand how temporal variability, resistance and overall ecosystem stability responded to diversity (that is, species richness) in a large experiment involving 690 micro-ecosystems sampled 19 times over 40 days, resulting in 12,939 samplings. Species richness increased temporal stability but decreased resistance to warming. Thus, two stability components covaried negatively along the diversity gradient. Previous biodiversity manipulation studies rarely reported such negative covariation despite general predictions of the negative effects of diversity on individual stability components³. Integrating our findings with the ecosystem multifunctionality concept revealed hump- and U-shaped effects of diversity on overall ecosystem stability. That is, biodiversity can increase overall ecosystem stability when biodiversity is low, and decrease it when biodiversity is high, or the opposite with a U-shaped relationship. The effects of diversity on ecosystem multifunctionality would also be hump- or U-shaped if diversity had positive effects on some functions and negative effects on others. Linking the ecosystem multifunctionality concept and ecosystem stability can transform the perceived effects of diversity on ecological stability and may help to translate this science into policy-relevant information.
Tracking antibiotic consumption patterns over time and across countries could inform policies to optimize antibiotic prescribing and minimize antibiotic resistance, such as setting and enforcing per capita consumption targets or aiding investments in alternatives to antibiotics. In this study, we analyzed the trends and drivers of antibiotic consumption from 2000 to 2015 in 76 countries and projected total global antibiotic consumption through 2030. Between 2000 and 2015, antibiotic consumption, expressed in defined daily doses (DDD), increased 65% (21.1-34.8 billion DDDs), and the antibiotic consumption rate increased 39% (11.3-15.7 DDDs per 1,000 inhabitants per day). The increase was driven by low- and middle-income countries (LMICs), where rising consumption was correlated with gross domestic product per capita (GDPPC) growth (P= 0.004). In high-income countries (HICs), although overall consumption increased modestly, DDDs per 1,000 inhabitants per day fell 4%, and there was no correlation with GDPPC. Of particular concern was the rapid increase in the use of last-resort compounds, both in HICs and LMICs, such as glycylcyclines, oxazolidinones, carbapenems, and polymyxins. Projections of global antibiotic consumption in 2030, assuming no policy changes, were up to 200% higher than the 42 billion DDDs estimated in 2015. Although antibiotic consumption rates in most LMICs remain lower than in HICs despite higher bacterial disease burden, consumption in LMICs is rapidly converging to rates similar to HICs. Reducing global consumption is critical for reducing the threat of antibiotic resistance, but reduction efforts must balance access limitations in LMICs and take account of local and global resistance patterns.
Human impacts on biodiversity are well recognized, but uncertainties remain regarding patterns of diversity change at different spatial and temporal scales. Changes in microbial assemblages are, in particular, not well understood, partly due to the lack of community composition data over relevant scales of space and time. Here, we investigate biodiversity patterns in cyanobacterial assemblages over one century of eutrophication and climate change by sequencing DNA preserved in the sediments of ten European peri-Alpine lakes. We found species losses and gains at the lake scale, while species richness increased at the regional scale over approximately the past 100 years. Our data show a clear signal for beta diversity loss, with the composition and phylogenetic structure of assemblages becoming more similar across sites in the most recent decades, as have the general environmental conditions in and around the lakes. We attribute patterns of change in community composition to raised temperatures affecting the strength of the thermal stratification and, as a consequence, nutrient fluctuations, which favoured cyanobacterial taxa able to regulate buoyancy. Our results reinforce previous reports of human-induced homogenization of natural communities and reveal how potentially toxic and bloom-forming cyanobacteria have widened their geographic distribution in the European temperate region.
Surveys of carbon: nitrogen: phosphorus ratios are available now for major groups of biota and for various aquatic and terrestrial biomes. However, while fungi play an important role in nutrient cycling in ecosystems, relatively little is known about their C:N:P stoichiometry and how it varies across taxonomic groups, functional guilds, and environmental conditions. Here we present the first systematic compilation of C:N:P data for fungi including four phyla (Ascomycota, Basidiomycota, Glomeromycota, and Zygomycota). The C, N, and P contents (percent of dry mass) of fungal biomass varied from 38% to 57%, 0.23% to 15%, and 0.040% to 5.5%, respectively. Median C:N:P stoichiometry for fungi was 250:16:1 (molar), remarkably similar to the canonical Redfield values. However, we found extremely broad variation in fungal C:N:P ratios around the central tendencies in C:N:P ratios. Lower C:P and N:P ratios were found in Ascomycota fungi than in Basidiomycota fungi while significantly lower C:N ratios (p<0.05) a
Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystemprocesses they regulate is unknown. We compare soilmicrobial communities frompaired reference and dairymanure-exposed sites across theUSA. Given thatmanure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the b-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundancewas positively correlatedwith indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold undermanure exposure. These findings demonstrate that themaintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function.
Despite our continuous improvement in understanding antibiotic resistance, the interplay between natural selection of resistance mutations and the environment remains unclear. To investigate the role of bacterial metabolism in constraining the evolution of antibiotic resistance, we evolved Escherichia coli growing on glycolytic or gluconeogenic carbon sources to the selective pressure of three different antibiotics. Profiling more than 500 intracellular and extracellular putative metabolites in 190 evolved populations revealed that carbon and energy metabolism strongly constrained the evolutionary trajectories, both in terms of speed and mode of resistance acquisition. To interpret and explore the space of metabolome changes, we developed a novel constraint?based modeling approach using the concept of shadow prices. This analysis, together with genome resequencing of resistant populations, identified condition?dependent compensatory mechanisms of antibiotic resistance, such as the shift from respiratory to fermentative metabolism of glucose upon overexpression of efflux pumps. Moreover, metabolome?based predictions revealed emerging weaknesses in resistant strains, such as the hypersensitivity to fosfomycin of ampicillin?resistant strains. Overall, resolving metabolic adaptation throughout antibiotic?driven evolutionary trajectories opens new perspectives in the fight against emerging antibiotic resistance.
Microorganisms are physiologically diverse, possessing disparate genomic features and mechanisms for adaptation (functional traits), which reflect on their associated life strategies and determine at least to some extent their prevalence and distribution in the environment. Unlike animals and plants, there is an unprecedented diversity and intractable metabolic versatility among bacteria, making classification or grouping these microorganisms based on their functional traits as has been done in animal and plant ecology challenging. Nevertheless, based on representative pure cultures, microbial traits distinguishing different life strategies had been proposed, and had been the focus of previous reviews. In the environment, however, the vast majority of naturally-occurring microorganisms have yet to be isolated, restricting the association of life strategies to broad phylogenetic groups and/or physiological characteristics. Here, we reviewed the literature to determine how microbial life strategy concepts (i.e. copio- and oligo-trophic strategist, and Competitor-Stress tolerator-Ruderals, CSR framework) are applied in complex microbial communities. Because of the scarcity of direct empirical evidence elucidating the associated life strategies in complex communities, we rely heavily on observational studies determining the response of microorganisms to (a)biotic cues (e.g. resource availability) to infer microbial life strategies. Although our focus is on the life strategies of bacteria, parallels were drawn from the fungal community. Our literature search showed inconsistency in the community response of proposed copiotrophic- and oligotrophic-associated microorganisms (phyla level) to changing environmental conditions. This suggests that tracking microorganisms at finer phylogenetic and taxonomic resolution (e.g. family level or lower) may be more effective to capture changes in community response and/or that edaphic factors exert a stronger effect in community response. We discuss the limitations, and provide recommendations for future research applying microbial life strategies in environmental studies.
The Intergovernmental Technical Panel on Soils has completed the first State of the World's Soil Resources Report. Globally soil erosion was identified as the gravest threat, leading to deteriorating water quality in developed regions and to lowering of crop yields in many developing regions. We need to increase nitrogen and phosphorus fertilizer use in infertile tropical and semi-tropical soils – the regions where the most food insecurity among us are found – while reducing global use of these products overall. Stores of soil organic carbon are critical in the global carbon balance, and national governments must set specific targets to stabilize or ideally increase soil organic carbon stores. Finally the quality of soil information available for policy formulation must be improved – the regional assessments in the State of the World's Soil Resources Report frequently base their evaluations on studies from the 1990s based on observations made in the 1980s or earlier.
Microbial carbon use efficiency (CUE) is a critical regulator of soil organic matter dynamics and terrestrial carbon fluxes, with strong implications for soil biogeochemistry models. While ecologists increasingly appreciate the importance of CUE, its core concepts remain ambiguous: terminology is inconsistent and confusing, methods capture variable temporal and spatial scales, and the significance of many fundamental drivers remains inconclusive. Here we outline the processes underlying microbial efficiency and propose a conceptual framework that structures the definition of CUE according to increasingly broad temporal and spatial drivers where (1) CUE
reflects population-scale carbon use efficiency of microbes governed by species-specific metabolic and thermodynamic constraints, (2) CUE
defines community-scale microbial efficiency as gross biomass production per unit substrate taken up over short time scales, largely excluding recycling of microbial necromass and exudates, and (3) CUE
reflects the ecosystem-scale efficiency of net microbial biomass production (growth) per unit substrate taken up as iterative breakdown and recycling of microbial products occurs. CUEE integrates all internal and extracellular constraints on CUE and hence embodies an ecosystem perspective that fully captures all drivers of microbial biomass synthesis and decay. These three definitions are distinct yet complementary, capturing the capacity for carbon storage in microbial biomass across different ecological scales. By unifying the existing concepts and terminology underlying microbial efficiency, our framework enhances data interpretation and theoretical advances.
The Intergovernmental Technical Panel on Soils has completed the first State of the World's Soil Resources report. Globally soil erosion was identified as the gravest threat, leading to deteriorating water quality in developed regions and to lowering of crop yields in many developing regions. We need to increase nitrogen and phosphorus fertilizer use in infertile tropical and semi-tropical soils – the regions where the most food insecure among us are found – while reducing global use of these products overall. Stores of soil organic carbon are critical in the global carbon balance, and national governments must set specific targets to stabilize or ideally increase soil organic carbon stores. Finally the quality of soil information available for policy formulation must be improved – the regional assessments in the SWSR report frequently base their evaluations on studies from the 1990s based on observations made in the 1980s or earlier.
Loss of biodiversity impacts ecosystem functions, such as carbon (C) cycling. Soils are the largest terrestrial C reservoir, containing more C globally than the biotic and atmospheric pools together. As such, soil C cycling, and the processes controlling it, has the potential to affect atmospheric CO2 concentrations and subsequent climate change. Despite the growing evidence of links between plant diversity and soil C cycling, there is a dearth of information on whether similar relationships exist between soil biodiversity and C cycling. This knowledge gap occurs even though there has been increased recognition that soil communities display high levels of both taxonomic and functional diversity and are key drivers of fluxes of C between the atmosphere and terrestrial ecosystems. Here, we used meta-analysis and regression analysis to quantitatively assess how soil biodiversity affects soil C cycling pools and processes (i.e., soil C respiration, litter decomposition, and plant biomass). We compared the response of process variables to changes in diversity both within and across groups of soil organisms that differed in body size, a grouping that typically correlates with ecological function. When studies that manipulated both within- and across-body size group diversity were included in the meta-analysis, loss of diversity significantly reduced soil C respiration (−27.5%) and plant tissue decomposition (−18%) but did not affect above- or belowground plant biomass. The loss of within-group diversity significantly reduced soil C respiration, while loss of across-group diversity did not. Decomposition was negatively affected both by loss of within-group and across-group diversity. Furthermore, loss of microbial diversity strongly reduced soil C respiration (−41%). In contrast, plant tissue decomposition was negatively affected by loss of soil faunal diversity but was unaffected by loss of microbial diversity. Taken together, our findings show that loss of soil biodiversity strongly impacts on soil C cycling processes, and highlight the importance of diversity across groups of organisms (e.g., primary consumers and secondary decomposers) for maintaining full functionality of C cycle processes. However, our understanding of the complex relationships between soil biodiversity and C cycling processes is currently limited by the sheer number of methodological concerns associated with these studies, which can greatly overestimate or underestimate the impact of soil biodiversity on soil C cycling, challenging extrapolation to natural field settings. Future studies should attempt to further elucidate the relative importance of taxonomic diversity (species numbers) versus functional diversity.
The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4(+)-N, NO3(-)-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift.
Cephapirin, a cephalosporin antibiotic, is used by the majority of dairy farms in the US. Fecal and urinary excretion of cephapirin could introduce this compound into the environment when manure is land applied as fertilizer, and may cause development of bacterial resistance to antibiotics critical for human health. The environmental loading of cephapirin by the livestock industry remains un-assessed, largely due to a lack of appropriate analytical methods. Therefore, this study aimed to develop and validate a cephapirin quantification method to capture the temporal pattern of cephapirin excretion in dairy cows following intramammary infusion. The method includes an extraction with phosphate buffer and methanol, solid-phase extraction (SPE) clean-up, and quantification using ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The LOQ values of the developed method were 4.02 µg kg-1 and 0.96 µg L-1 for feces and urine, respectively. This robust method recovered >60% and >80% cephapirin from spiked blank fecal and urine samples, respectively, with acceptable intra- and inter-day variation (<10%). Using this method, we detected trace amounts (µg kg-1) of cephapirin in dairy cow feces, and cephapirin in urine was detected at very high concentrations (133 to 480 µg L-1). Cephapirin was primarily excreted via urine and its urinary excretion was influenced by day (P = 0.03). Peak excretion (2.69 mg) was on day 1 following intramammary infusion and decreased sharply thereafter (0.19, 0.19, 0.08, and 0.17 mg on day 2, 3, 4, and 5, respectively) reflecting a quadratic pattern of excretion (Quadratic: P = 0.03). The described method for quantification of cephapirin in bovine feces and urine is sensitive, accurate, and robust and allowed to monitor the pattern of cephapirin excretion in dairy cows. This data will help develop manure segregation and treatment methods to minimize the risk of antibiotic loading to the environment from dairy farms.
Antibiotic resistance is increasing in pathogenic microbial populations and is thus a major threat to public health. The fate of a resistance mutation in pathogen populations is determined in part by its fitness. Mutations that suffer little or no fitness cost are more likely to persist in the absence of antibiotic treatment. In this review, we performed a meta-analysis to investigate the fitness costs associated with single mutational events that confer resistance. Generally, these mutations were costly, although several drug classes and species of bacteria on average did not show a cost. Further investigations into the rate and fitness values of compensatory mutations that alleviate the costs of resistance will help us to better understand both the emergence and management of antibiotic resistance in clinical settings.
Maximum likelihood or restricted maximum likelihood (REML) estimates of the
parameters in linear mixed-effects models can be determined using the lmer
function in the lme4 package for R. As for most model-fitting functions in R,
the model is described in an lmer call by a formula, in this case including
both fixed- and random-effects terms. The formula and data together determine a
numerical representation of the model from which the profiled deviance or the
profiled REML criterion can be evaluated as a function of some of the model
parameters. The appropriate criterion is optimized, using one of the
constrained optimization functions in R, to provide the parameter estimates. We
describe the structure of the model, the steps in evaluating the profiled
deviance or REML criterion, and the structure of classes or types that
represents such a model. Sufficient detail is included to allow specialization
of these structures by users who wish to write functions to fit specialized
linear mixed models, such as models incorporating pedigrees or smoothing
splines, that are not easily expressible in the formula language used by lmer.
Tetracyclines are antibiotics commonly used in swine farms to treat disease and promote growth. However, there are growing concerns regarding the discharge of animal feces into the environment owing to the potential for development and dissemination of tetracycline resistance genes (TRGs). In this study, farming wastewater from one Chinese swine farm as well as river water from seven locations downstream of the farm was sampled. Polymerase chain reaction (PCR) showed that 12 TRGs, including six efflux pump genes (tet(B), tet(C), tet(D), tet(E), tet(G) and tet(L)), five ribosomal protection proteins (RPPs) genes (tet(O), tet(M), tet(Q), tet(W) and tet(S)), and one enzymatic modification gene (tet(X)), were present in all wastewater and river water samples. Quantitative real-time PCR (qPCR) showed that the abundance of tet(C), tet(X), tet(O), tet(M), tet(Q) and tet(W) decreased with downstream flow. Among the detected TRGs, tet(C) had the highest abundance, ranging from 459.5 copies/16S rRNA gene copies in wastewater to 33.8 copies/16S rRNA gene copies in river water samples collected from the last location. Furthermore, pig-specific Bacteroidales 16S rRNA genetic marker was quantified by qPCR to determine the level of fecal pollution in the river water. Bivariate correlation analysis confirmed that the total relative abundance of the six TRGs was significantly correlated with the level of swine feces in the aquatic environment (R(2) = 0.63, P < 0.05), suggesting that swine feces mainly contributed to the spread of TRGs in the river water. Supplemental materials are available for this article. Go to the publisher's online edition of Journal of Environmental Science and Health, Part A to view the free supplemental file.
Interspecies interaction is an essential mechanism for bacterial communities to develop antibiotic resistance via horizontal gene transfer. Nonetheless, how bacterial interactions vary along the environmental transmission of antibiotics and the underpinnings remain unclear. To address it, we explore potential microbial associations by analyzing bacterial networks generated from 16S rRNA gene sequences and functional networks containing a large number of antibiotic-resistance genes (ARGs). Antibiotic concentration decreased by more than 4000-fold along the environmental transmission chain from manure samples of swine farms to aerobic compost, compost-amended agricultural soils, and neighboring agricultural soils. Both bacterial and functional networks became larger in nodes and links with decreasing antibiotic concentrations, likely resulting from lower antibiotics stress. Nonetheless, bacterial networks became less clustered with decreasing antibiotic concentrations, while functional networks became more clustered. Modularity, a key topological property that enhances system resilience to antibiotic stress, remained high for functional networks, but the modularity values of bacterial networks were the lowest when antibiotic concentrations were intermediate. To explain it, we identified a clear shift from deterministic processes, particularly variable selection, to stochastic processes at intermediate antibiotic concentrations as the dominant mechanism in shaping bacterial communities. Collectively, our results revealed microbial network dynamics and suggest that the modularity value of association networks could serve as an important indicator of antibiotic concentrations in the environment.
Biocides have been frequently used to understand the roles of fungi and bacteria on soil carbon (C) and nitrogen (N) cycling. However, addition of biocides to soil can result in unwanted temporary increases in C and N supply to surviving microbes due to a pulse in microbial necromass, and where biocides can directly be used as sources of C and N. We assessed temporary dynamics in microbial biomass C (MBC) and N (MBN), soil respiration and gross N mineralization (GNM) during a 22-day laboratory incubation after addition of fungicides (captan, cycloheximide) and bactericides (bronopol, oxytetracycline) in a grassland soil. We also assessed whether captan and bronopol were a C source for remaining microbes based on δ 13 C measurements in respired CO 2. As expected, fungicides decreased and bactericides increased fungi:bacteria ratios, while all biocides decreased MBC and MBN. However, respiration (except for oxytetracycline) and GNM (particularly for bronopol) increased after biocide addition, likely because of a pulse in necromass causing increased substrate supply to the surviving microbes. We further detected biocide-derived CO 2 up to 10 days for captan, and 22 days for bronopol, suggesting that they can be an important source for C by surviving microbes. However, soil-derived CO 2 remained higher without biocide, indicating that necromass was the most important source for higher soil respiration after biocide addition. We recommend repeated additions of biocides to suppress regrowth of target microbes, and use of 13 C and 15 N labeled substrates, when studying effects of fungi and bacteria on C and N dynamics.
Regions and localities may lose many species to extinction under rapid climate change and may gain other species that colonize from nearby warmer environments. Here, it is argued that warming-induced species losses will generally exceed gains and there will be more net declines than net increases in plant community richness. Declines in richness are especially likely in water-limited climates where intensifying aridity will increasingly exceed plant tolerances, but also in colder temperature-limited climates where steep climatic gradients are lacking, and therefore, large pools of appropriate species are not immediately adjacent. The selectivity of warming-induced losses may lead to declines in functional and phylogenetic diversity as well as in species richness, especially in water-limited climates. Our current understanding of climate-caused diversity trends may be overly influenced by numerous studies coming from north-temperate alpine mountaintops, where conditions are unusually favourable for increases—possibly temporary—in local species richness.
This article is part of the theme issue ‘Climate change and ecosystems: threats, opportunities and solutions’.
Soils underpin terrestrial ecosystem functions, but they face numerous anthropogenic pressures. Despite their crucial ecological role, we know little about how soils react to more than two environmental factors at a time. Here, we show experimentally that increasing the number of simultaneous global change factors (up to 10) caused increasing directional changes in soil properties, soil processes, and microbial communities, though there was greater uncertainty in predicting the magnitude of change. Our study provides a blueprint for addressing multifactor change with an efficient, broadly applicable experimental design for studying the impacts of global environmental change.
The soil microbiome governs biogeochemical cycling of macronutrients, micronutrients and other elements vital for the growth of plants and animal life. Understanding and predicting the impact of climate change on soil microbiomes and the ecosystem services they provide present a grand challenge and major opportunity as we direct our research efforts towards one of the most pressing problems facing our planet. In this Review, we explore the current state of knowledge about the impacts of climate change on soil microorganisms in different climate-sensitive soil ecosystems, as well as potential ways that soil microorganisms can be harnessed to help mitigate the negative consequences of climate change.
Predictions of the effects of global change on ecological communities are largely based on single habitats. Yet in nature, habitats are interconnected through the exchange of energy and organisms, and the responses of local communities may not extend to emerging community networks (i.e. metacommunities). Using large mesocosms and meiofauna communities as a model system, we investigated the interactive effects of ocean warming and acidification on the structure of marine metacommunities from three shallow‐water habitats: sandy soft‐bottoms, marine vegetation and rocky reef substrates. Primary producers and detritus – key food sources for meiofauna – increased in biomass under the combined effect of temperature and acidification. The enhanced bottom‐up forcing boosted nematode densities but impoverished the functional and trophic diversity of nematode metacommunities. The combined climate stressors further homogenized meiofauna communities across habitats. Under present‐day conditions metacommunities were structured by habitat type, but under future conditions they showed an unstructured random pattern with fast‐growing generalist species dominating the communities of all habitats. Homogenization was likely driven by local species extinctions, reducing interspecific competition that otherwise could have prevented single species from dominating multiple niches. Our findings reveal that climate change may simplify metacommunity structure and prompt biodiversity loss, which may affect the biological organization and resilience of marine communities.
We examined the impacts of soil moisture, temperature, agricultural management, and habitat type on the degradation dynamics of eDNA in soils. Synthetic eDNA was added to soil microcosms, and its disappearance over time was measured using both high‐throughput sequencing and qPCR. The synthetic eDNA was degraded rapidly, but a small fraction remained detectable throughout the experiments (39‐80 days). The eDNA degradation rate was positively correlated with moisture and temperature, but negatively correlated with soil organic carbon content. End‐point stabilization of eDNA was highest at low moisture and temperature, but exhibited no relationship with soil organic carbon. Tilled soils had higher rates of degradation and less stabilization than no‐till soils. Among different habitats we observed that forest soils had the slowest degradation rate, and meadow soils had the greatest stabilization of eDNA. While eDNA was detectable by qPCR in all treatments across all time‐points, it became inconsistently detectable with high‐throughput gene sequencing in less than one week. We conclude that eDNA degradation and stabilization dynamics vary with moisture, temperature, and habitat characteristics, that small amounts of eDNA may persist in soils indefinitely, and that the ability of persistent eDNA to impact microbial community estimates depends on method sensitivity and experimental objectives.
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Models representing exchange of carbon between the atmosphere and the terrestrial biosphere include a large variety of processes and mechanisms, and have increased in complexity in the last decades. These models are no exception of the simulation versus understanding conundrum previously articulated for models of the physical climate, which states that increasing detail in process representation in models, and the simulations they produce, hinders understanding of holistic system behavior. However, recent theoretical progress on the mathematical representation of the carbon cycle in ecosystems may help to provide a general framework for the qualitative understanding of models without compromising detail in process representation. Here we (1) briefly review recent ideas on the theory of transient dynamics of the terrestrial carbon cycle and its matrix representation, pointing out issues of interpretation, (2) show that these ideas can be further generalized in the mathematical concept of nonautonomous compartmental systems, and (3) provide thoughts on how this framework can be used to address a new set of questions in carbon cycle science.
The relationship between the spatial variability of soil multifunctionality (i.e. the capacity of soils to conduct multiple functions; SVM) and major climatic drivers, such as temperature and aridity, has never been assessed globally in terrestrial ecosystems. We surveyed 236 dryland ecosystems from six continents to evaluate the relative importance of aridity and mean annual temperature, and of other abiotic (e.g., texture) and biotic (e.g., plant cover) variables as drivers of SVM, calculated as the averaged coefficient of variation for multiple soil variables linked to nutrient stocks and cycling. We found that increases in temperature and aridity were globally correlated to increases in SVM. Some of these climatic effects on SVM were direct, but others were indirectly driven through reductions in the number of vegetation patches and increases in soil sand content. The predictive capacity of our structural equation modelling was clearly higher for the spatial variability of N- than for C- and P- related soil variables. In the case of N cycling, the effects of temperature and aridity were both direct and indirect via changes in soil properties. For C and P, the effect of climate was mainly indirect via changes in plant attributes. These results suggest that future changes in climate may decouple the spatial availability of these elements for plants and microbes in dryland soils. Our findings significantly advance our understanding of the patterns and mechanisms driving SVM in drylands across the globe, which is critical for predicting changes in ecosystem functioning in response to climate change. Key words: Multifunctionality; carbon cycling; nitrogen cycling; phosphorous cycling; spatial heterogeneity; climate change This article is protected by copyright. All rights reserved.
Among the different pharmaceuticals present in soil and water ecosystems as micro-contaminants, considerable attention has been paid to antibiotics, since their increasing use and the consequent development of multi-resistant bacteria pose serious risks to human and veterinary health. Moreover, once they have entered the environment, antibiotics can affect natural microbial communities. The latter play a key role in fundamental ecological processes, most importantly the maintenance of soil and water quality. In fact, they are involved in biogeochemical cycling and organic contaminant degradation thanks to their large reservoir of genetic diversity and metabolic capability. When antibiotics occur in the environment, they can hamper microbial community structure and functioning in different ways and have both direct (short-term) and indirect (long-term) effects on microbial communities. The short-term ones are bactericide and bacteriostatic actions with a consequent disappearance of some microbial populations and their ecological functioning. The indirect impact includes the development of antibiotic resistant bacteria and in some cases bacterial strains able to degrade them by metabolic or co-metabolic processes. Biodegradation makes it possible to completely remove a toxic compound from the environment if it is mineralized.Several factors can influence the significance of such direct and indirect effects, including the antibiotic's concentration, the exposure time, the receiving ecosystem (e.g. soil or water) and the co-occurrence of other antibiotics and/or other contaminants.This review describes the current state of knowledge regarding the effects of antibiotics on natural microbial communities in soil and water ecosystems.
Manure composting has general benefits for production of soil amendment, but the effects of composting on antibiotic persistence and effects of antibiotics on the composting process are not well-characterized, especially for antibiotics commonly used in dairy cattle. This study provides a comprehensive, head-to-head, replicated comparison of the effect of static and turned composting on typical antibiotics used in beef and dairy cattle in their actual excreted form and corresponding influence on composting efficacy. Manure from steers (with or without chlortetracycline, sulfamethazine, and tylosin feeding) and dairy cows (with or without pirlimycin and cephapirin administration) were composted at small scale (wet mass: 20-22 kg) in triplicate under static and turned conditions adapted to represent US Food and Drug Administration guidelines. Thermophilic temperature (>55°C) was attained and maintained for 3 d in all composts, with no measureable effect of compost method on the pattern, rate, or extent of disappearance of the antibiotics examined, except tylosin. Disappearance of all antibiotics, except pirlimycin, followed bi-phasic first-order kinetics. However, individual antibiotics displayed different fate patterns in response to the treatments. Reduction in concentration of chlortetracycline (71-84%) and tetracycline (66-72%) was substantial, while near-complete removal of sulfamethazine (97-98%) and pirlimycin (100%) was achieved. Tylosin removal during composting was relatively poor. Both static and turned composting were generally effective for reducing most beef and dairy antibiotic residuals excreted in manure, with no apparent negative impact of antibiotics on the composting process, but with some antibiotics apparently more recalcitrant than others.
During the past decade pharmaceuticals have been recognised as a new class of ubiquitously occurring persistent contaminants (Halling-Sørensen et al. 1998; Daughton and Ternes 1999; Kämmerer 2001; Boxall et al. 2003; Diaz-Cruz et al. 2003; Thiele-Bruhn 2003). A large number of drugs are used extensively in both human and veterinary medicine. Antibiotics are one of the most important substance classes with a possible environmental impact. Estimations of the European Federation of Animal Health (FEDESA) revealed that approximately 8500 tons of antibiotics were used in human medicine and 4700 tons in veterinary medicine in the European Union (including Switzerland) in 1999 (Anonymous 2001).
Fungal community composition often shifts in response to warmer temperatures, which might influence decomposition of recalcitrant carbon (C). We hypothesized that evolutionary trade-offs would enable recalcitrant C-using taxa to respond more positively to warming than would labile C-using taxa. Accordingly, we performed a warming experiment in an Alaskan boreal forest and examined changes in the prevalence of fungal taxa. In a complementary field trial, we characterized the ability of fungal taxa to use labile C (glucose), intermediate C (hemicellulose or cellulose), or recalcitrant C (lignin). We also assigned taxa to functional groups (e.g., free-living filamentous fungi, ectomycorrhizal fungi, and yeasts) based on taxonomic identity. We found that response to warming varied most among taxa at the order level, compared to other taxonomic ranks. Among orders, ability to use lignin was significantly related to increases in prevalence in response to warming. However, the relationship was weak, given that lignin use explained only 9% of the variability in warming responses. Functional groups also differed in warming responses. Specifically, free-living filamentous fungi and ectomycorrhizal fungi responded positively to warming, on average, but yeasts responded negatively. Overall, warming-induced shifts in fungal communities might be accompanied by an increased ability to break down recalcitrant C. This change in potential function may reduce soil C storage under global warming.
The human gut harbors a large and complex community of beneficial microbes that remain stable over long periods. This stability is considered critical for good health but is poorly understood. Here we develop a body of ecological theory to help us understand microbiome stability. Although cooperating networks of microbes can be efficient, we find that they are often unstable. Counterintuitively, this finding indicates that hosts can benefit from microbial competition when this competition dampens cooperative networks and increases stability.More generally, stability is promoted by limiting positive feedbacks and weakening ecological interactions. We have analyzed host mechanisms formaintaining stability - including immune suppression, spatial structuring, and feeding of community members - and support our key predictions with recent data.
Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large scale has resulted in poor understanding of how soil biodiversity could be incorporated into legislation for the protection of soil quality. In 2011, the EcoFINDERS (FP7) project sampled 76 sites across 11 European countries, covering five biogeographical zones (Alpine, Atlantic, Boreal, Continental and Mediterranean) and three land-uses (arable, grass, forestry). Samples collected from across these sites ranged in soil properties; soil organic carbon (SOC), pH and texture. To assess the range in biodiversity and ecosystem function across the sites, fourteen biological methods were applied as proxy indicators for these functions. These methods measured the following: microbial diversity: DNA yields (molecular biomass), archaea, bacteria, total fungi and arbuscular mycorrhizal fungi; micro fauna diversity: nematode trophic groups; meso fauna diversity: enchytraeids and Collembola species; microbial function: nitrification, extracellular enzymes, multiple substrate induced respiration, community level physiological profiling and ammonia oxidiser/nitrification functional genes. Network analysis was used to identify the key connections between organisms under the different land use scenarios. Highest network density was found in forest soils and lowest density occurred in arable soils. Key taxomonic units (TUs) were identified in each land-use type and in relation to SOC and pH categorisations. Top-connected taxonomic units (i.e. displaying the most co-occurrence to other TUs) were identified for each land use type. In arable sites this was dominated by bacteria and fungi, while in grassland sites bacteria and fungi were most connected. In forest soils archaeal, enchytraeid and fungal TUs displayed the largest number of neighbours, reflecting the greatest connectivity. Multiple regression models were applied to assess the potential contribution of soil organisms to carbon cycling and storage and nutrient cycling of specifically nitrogen and phosphorus. Key drivers of carbon cycling were microbial biomass, basal respiration and fungal richness; these three measures have often been associated with carbon cycling in soils. Regression models of nutrient cycling were dependent on the model applied, showing variation in biological indicators.
Veterinary medicines are used widely to treat disease and protect the health of animals. Following administration, veterinary medicines may be metabolised and then released along with any metabolites either directly to the environment (as is the case with pasture animals) or indirectly during the application of manure or slurry.
Resolving fungal and bacterial groups within the microbial decomposer
community is thought to capture disparate life strategies for soil microbial decomposers,
associating bacteria with an r-selected strategy for carbon (C) and nutrient use, and fungi
with a K-selected strategy. Additionally, food-web model-based work has established a widely
held belief that the bacterial decomposer pathway in soil supports high turnover rates of
easily available substrates, while the slower fungal-dominated decomposition pathway
supports the decomposition of more complex organic material, thus characterizing the
biogeochemistry of the ecosystem. We used a field experiment, the Detritus Input and
Removal Treatments, or DIRT, experiment (Harvard Forest Long-Term Ecological
Research Site, USA) where litter and root inputs (control, no litter, double litter, or no
tree roots) have been experimentally manipulated during 23 years, generating differences in
soil C quality. We hypothesized (1) that d13C enrichment would decrease with higher soil C
quality and that a higher C quality would favor bacterial decomposers, (2) that the C
mineralized in fungal-dominated treatments would be of lower quality and also depleted in
d13C relative to bacterial-dominated high-quality soil C treatments, and (3) that higher C
mineralization along with higher gross N mineralization rates would occur in bacterialdominated
treatments compared with more fungal-dominated treatments. The DIRT
treatments resulted in a gradient of soil C quality, as shown by up to 4.5-fold differences
between the respiration per soil C between treatments. High-quality C benefited fungal
dominance, in direct contrast with our hypothesis. Further, there was no difference between
the d13CO2 produced by a fungal compared with a bacterial-dominated decomposer
community. There were differences in C and N mineralization between DIRT treatments, but
these were not related to the relative dominance of fungal and bacterial decomposers. Thus
we find no support for the hypothesized differences between detrital food webs dominated by
bacteria compared to those dominated by fungi. Rather, an association between high-quality
soil C and fungi emerges from our results. Consequently there is a need to revise our basic
understanding for microbial communities and the processes they regulate in soil.
Biofuels will help meet rising demands for energy and, ideally, limit climate change associated with carbon losses from the biosphere to atmosphere. Biofuel management must therefore maximize energy production and maintain ecosystem carbon stocks. Increasingly, there is interest in intercropping biofuels with other crops, partly because biofuel production on arable land might reduce availability and increase the price of food. One intercropping approach involves growing biofuel grasses in forest plantations. Grasses differ from trees in both their organic inputs to soils and microbial associations. These differences are associated with losses of soil carbon when grasses become abundant in forests. We investigated how intercropping switchgrass (Panicum virgatum), a major candidate for cellulosic biomass production, in loblolly pine (Pinus taeda) plantations affects soil carbon, nitrogen, and microbial dynamics. Our design involved four treatments: two pine management regimes where harvest residues (i.e., biomass) were left in place or removed, and two switchgrass regimes where the grass was grown with pine under the same two biomass scenarios (left or removed). Soil variables were measured in four 1-ha replicate plots in the first and second year following switchgrass planting. Under switchgrass intercropping, pools of mineralizable and particulate organic matter carbon were 42% and 33% lower, respectively. These declines translated into a 21% decrease in total soil carbon in the upper 15 cm of the soil profile, during early stand development. The switchgrass effect, however, was isolated to the interbed region where switchgrass is planted. In these regions, switchgrass-induced reductions in soil carbon pools with 29%, 43%, and 24% declines in mineralizable, particulate, and total soil carbon, respectively. Our results support the idea that grass inputs to forests can prime the activity of soil organic carbon degrading microbes, leading to net reductions in stocks of soil carbon. Active microbial biomass, however, is higher under switchgrass, and this microbial biomass is a dominant precursor of soil carbon formation. Future studies need to investigate soil carbon dynamics throughout the lifetime of intercropping rotations to evaluate whether increases in microbial biomass can offset initial declines in soil carbon, and hence, maintain ecosystem carbon stocks.
One of the key questions in climate change research relates to the future dynamics of the large amount of C that is currently stored in soil organic matter. Will the amount of C in this pool increase or decrease with global warming? The future trend in amounts of soil organic C will depend on the relative temperature sensitivities of net primary productivity and soil organic matter decomposition rate. Equations for the temperature dependence of net primary productivity have been widely used, but the temperature dependence of decomposition rate is less clear. The literature was surveyed to obtain the temperature dependencies of soil respiration and N dynamics reported in different studies. Only laboratory-based measurements were used to avoid confounding effects with differences in litter input rates, litter quality, soil moisture or other environmental factors. A considerable range of values has been reported, with the greatest relative sensitivity of decomposition processes to temperature having been observed at low temperatures. A relationship fitted to the literature data indicated that the rate of decomposition increases with temperature at 0°C with a Q10 of almost 8. The temperature sensitivity of organic matter decomposition decreases with increasing temperature, indicated by the Q10 decreasing with temperature to be about 4.5 at 10°C and 2.5 at 20°C. At low temperatures, the temperature sensitivity of decomposition was consequently much greater than the temperature sensitivity of net primary productivity, whereas the temperature sensitivities became more similar at higher temperatures. The much higher temperature sensitivity of decomposition than for net primary productivity has important implications for the store of soil organic C in the soil. The data suggest that a 1°C increase in temperature could ultimately lead to a loss of over 10% of soil organic C in regions of the world with an annual mean temperature of 5°C, whereas the same temperature increase would lead to a loss of only 3% of soil organic C for a soil at 30°C. These differences are even greater in absolute amounts as cooler soils contain greater amounts of soil organic C. This analysis supports the conclusion of previous studies which indicated that soil organic C contents may decrease greatly with global warming and thereby provide a positive feed-back in the global C cycle.
The future of the land carbon sink is a significant uncertainty in global change projections. Here, key controls on global terrestrial carbon storage are examined using a simple model of vegetation and soil. Equilibrium solutions are derived as a function of atmospheric CO2 and global temperature, these environmental variables are then linked in an idealized global change trajectory, and the lag between the dynamic and equilibrium solutions is derived for different linear rates of increase in atmospheric CO2. Terrestrial carbon storage is departing significantly from equilibrium because CO2 and temperature are increasing on a similar timescale to ecosystem change, and the lag is found to be proportional to the rate of forcing. Thus peak sizes of the land carbon sink, and any future land carbon source, are proportional to the rate of increase of CO2. A switch from a land carbon sink to a source occurs at a higher CO2 and temperature under more rapid forcing. The effects of parameter uncertainty in temperature sensitivities of photosynthesis, plant respiration and soil respiration, and structural uncertainty through the effect of fixing the ratio of plant respiration to photosynthesis are explored. In each case, the CO2 fertilization effect on photosynthesis is constrained to reproduce the 1990 atmospheric CO2 concentration within a closed global model. New literature compilations are presented for the temperature sensitivities of plant and soil respiration. A lower limit, Q10=1.29, for soil respiration significantly increases future land carbon storage. An upper limit, Q10=3.63, for soil respiration underpredicts the increase in carbon storage since the Last Glacial Maximum. Fixing the ratio of plant respiration to photosynthesis (R/P) at 0.5 generates the largest and most persistent land carbon sink, followed by the weakest land carbon source.