Soil microorganisms act as gatekeepers for soil-atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible ...hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates.
Soil microbial communities regulate global biogeochemical cycles and respond rapidly to changing environmental conditions. However, understanding how soil microbial communities respond to climate ...change, and how this influences biogeochemical cycles, remains a major challenge. This is especially pertinent in alpine regions where climate change is taking place at double the rate of the global average, with large reductions in snow cover and earlier spring snowmelt expected as a consequence. Here, we show that spring snowmelt triggers an abrupt transition in the composition of soil microbial communities of alpine grassland that is closely linked to shifts in soil microbial functioning and biogeochemical pools and fluxes. Further, by experimentally manipulating snow cover we show that this abrupt seasonal transition in wide-ranging microbial and biogeochemical soil properties is advanced by earlier snowmelt. Preceding winter conditions did not change the processes that take place during snowmelt. Our findings emphasise the importance of seasonal dynamics for soil microbial communities and the biogeochemical cycles that they regulate. Moreover, our findings suggest that earlier spring snowmelt due to climate change will have far reaching consequences for microbial communities and nutrient cycling in these globally widespread alpine ecosystems.
There is an emerging consensus that microbial necromass carbon is the primary constituent of stable soil carbon, yet the controls on the stabilization process are unknown. Prior to stabilization, ...microbial necromass may be recycled by the microbial community. We propose that the efficiency of this recycling is a critical determinant of soil carbon stabilization rates. Here we explore the controls on necromass recycling efficiency in 27 UK grassland soils using stable isotope tracing and indicator species analysis. We found that recycling efficiency was unaffected by land management. Instead, recycling efficiency increased with microbial growth rate on necromass, and was highest in soils with low historical precipitation. We identified bacterial and fungal indicators of necromass recycling efficiency, which could be used to clarify soil carbon stabilization mechanisms. We conclude that environmental and microbial controls have a strong influence on necromass recycling, and suggest that this, in turn, influences soil carbon stabilization.
Microbial necromass recycling, which can influence soil carbon stabilization, is controlled by microbial growth and precipitation, as indicated by stable isotope tracing and indicator species analysis in a range of UK grasslands.
In Southeast Asia, oil palm (OP) plantations have largely replaced
tropical forests. The impact of this shift in land use on greenhouse gas
(GHG) fluxes remains highly uncertain, mainly due to a ...relatively small pool
of available data. The aim of this study is to quantify differences of
nitrous oxide (N2O) and methane (CH4) fluxes as well as soil
carbon dioxide (CO2) respiration rates from logged forests, oil palm
plantations of different ages, and an adjacent small riparian area. Nitrous
oxide fluxes are the focus of this study, as these emissions are expected to
increase significantly due to the nitrogen (N) fertilizer application in the
plantations. This study was conducted in the SAFE (Stability of Altered
Forest Ecosystems) landscape in Malaysian Borneo (Sabah) with measurements
every 2 months over a 2-year period. GHG fluxes were measured by static
chambers together with key soil physicochemical parameters and microbial
biodiversity. At all sites, N2O fluxes were spatially and temporally
highly variable. On average the largest fluxes (incl. 95 % CI) were measured
from OP plantations (45.1 (24.0–78.5) µg m−2 h−1 N2O-N), slightly smaller fluxes from the riparian area (29.4 (2.8–84.7) µg m−2 h−1 N2O-N), and the smallest fluxes from logged forests
(16.0 (4.0–36.3) µg m−2 h−1 N2O-N). Methane fluxes
were generally small (mean ± SD): −2.6 ± 17.2 µg CH4-C m−2 h−1 for OP and 1.3 ± 12.6 µg CH4-C m−2 h−1 for riparian, with the range of measured CH4 fluxes
being largest in logged forests (2.2 ± 48.3 µg CH4-C m−2 h−1). Soil respiration rates were larger from riparian areas
(157.7 ± 106 mg m−2 h−1 CO2-C) and logged forests
(137.4 ± 95 mg m−2 h−1 CO2-C) than OP plantations
(93.3 ± 70 mg m−2 h−1 CO2-C) as a result of larger
amounts of decomposing leaf litter. Microbial communities were distinctly
different between the different land-use types and sites. Bacterial
communities were linked to soil pH, and fungal and eukaryotic communities were linked to
land use. Despite measuring a large number of environmental parameters,
mixed models could only explain up to 17 % of the variance of measured
fluxes for N2O, 3 % of CH4, and 25 % of soil respiration.
Scaling up measured N2O fluxes to Sabah using land areas for forest and
OP resulted in emissions increasing from 7.6 Mt (95 % confidence interval,
−3.0–22.3 Mt) yr−1 in 1973 to 11.4 Mt (0.2–28.6 Mt) yr−1 in 2015 due
to the increasing area of forest converted to OP plantations over the last
∼ 40 years.
High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. ...However, current analytical approaches are of limited use in formalizing syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterize taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from survey metadata. Specifically, we modeled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on both the shape of landscape scale pH-abundance responses, and pH optima (pH at which OTU abundance is maximal). We identify that most of the soil OTUs examined exhibited a non-flat relationship with soil pH. Further, the pH optima could not be generalized by broad taxonomy, highlighting the need for tools and databases synthesizing ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (
https://shiny-apps.ceh.ac.uk/ID-TaxER/
), and flat files are made available for use in bioinformatic pipelines. The further development of advanced informatics infrastructures incorporating modeled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios.
Nanomaterials (NMs) can interact with the innate immunity of organisms. It remains, however, unclear whether these interactions can compromise the immune functioning of the host when faced with a ...disease threat. Co-exposure with pathogens is thus a powerful approach to assess the immuno-safety of NMs. In this paper, we studied the impacts of in vivo exposure to a biocidal NM on the gut microbiome, host immune responses, and susceptibility of the host to a bacterial challenge in an earthworm.
were exposed to CuO-nanoparticles in soil for 28 days, after which the earthworms were challenged with the soil bacterium
. Immune responses were monitored by measuring mRNA levels of known earthworm immune genes. Effects of treatments on the gut microbiome were also assessed to link microbiome changes to immune responses. Treatments caused a shift in the earthworm gut microbiome. Despite these effects, no impacts of treatment on the expression of earthworm immune markers were recorded. The methodological approach applied in this paper provides a useful framework for improved assessment of immuno-safety of NMs. In addition, we highlight the need to investigate time as a factor in earthworm immune responses to NM exposure.
Microorganisms are widely distributed throughout the built environment and even those found in concealed environments such as sink P‐traps can have an impact on our health. To date, most studies on ...sink bacterial communities focused on those present in hospitals with no to little information regarding sinks in residential or communal settings. Here, we conducted a characterization using 16S rRNA sequencing of the bacterial communities of communal restroom sinks located on a university campus to investigate the diversity, prevalence, and abundances of the bacteria that reside in this understudied environment. The study found that community composition and structure were highly variable across individual sinks, and there were marginal differences between buildings and the two different parts of sink examined. Proteobacteria were the most abundant phylum in the sink communities, and the families Burkholderiaceae, Moraxellaceae, and Sphingomonadaceae were found to be ubiquitous across all sinks. Notably, human skin was identified as a primary contributor to the below‐strainer sink bacterial community. These data provide novel insight into the sink bacterial communities' constituents and serve as the foundation for subsequent studies that might explore community stability and resilience of in situ sinks.
A characterization using 16S rRNA sequencing of the bacterial communities of communal restroom sinks located on a university campus to investigate the diversity, prevalence, and abundances of the bacteria. The study found that community composition and structure were highly variable across individual sinks, and there were marginal differences between buildings and the two different parts of sink examined, while Proteobacteria were the most abundant phylum in the sink communities. Notably, human skin was identified as a primary contributor to the below‐strainer sink bacterial community.
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.
Soil organic carbon (SOC) is a soil health indicator and understanding dynamics changing SOC stocks will help achieving net zero goals. Here we present four datasets featuring 11,750 data points ...covering co-located aboveground and below-ground metrics for exploring ecosystem SOC dynamics. Five sites across England with an established land use contrast, grassland and woodland next to each other, were rigorously sampled for aboveground (n = 109), surface (n = 33 soil water release curves), topsoil, and subsoil metrics. Commonly measured soil metrics were analysed in five soil increments for 0-1 metre (n = 4550). Less commonly measured soil metrics which were assumed to change across the soil profile were measured on a subset of samples only (n = 3762). Additionally, we developed a simple method for soil organic matter fractionation using density fractionation which is part of the less common metrics. Finally, soil metrics which may impact SOC dynamics, but with less confidence as to their importance across the soil profile were only measured on topsoil (~5-15 cm = mineral soil) and subsoil (below 50 cm) samples (n = 2567).
Bioluminescence in beetles is dependent upon the enzyme luciferase. It has been hypothesised luciferase evolved from a fatty acyl-CoA synthetase gene deriving a novel bioluminescent function ...(neofunctionalization) after a gene duplication event. We evaluated this hypothesis within a phylogenetic framework using independent evidence obtained from the genome of
Tribolium castaneum, published luciferase genes and novel luciferase and luciferase-like sequences. This phylogenetic study provides evidence for a large gene family of luciferase and luciferase-like paralogues in bioluminescent and non-bioluminescent beetles. All luciferase sequences formed a clade supporting a protoluciferase existing prior to the divergence of the Lampyridae, Elateridae and Phengodidae (Elateroidea). Multiple luciferase genes were identified from members of the Photurinae and the Luciolinae indicating complex gene duplication events within lampyrid genomes. The majority of luciferase residues were identified to be under purifying selection as opposed to positive selection. We conclude that beetle luciferase may have arisen from a process of subfunctionalization as opposed to neofunctionalization early on in the evolution of the Elateroidea.
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