Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter

Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems

The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.

Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome

There is increasing interest in further developing the plant protection product (PPP) environmental risk assessment, particularly within the European Union, to include the assessment of soil microbial community composition, as measured by metabarcoding approaches. However, to date, there has been little discussion as to how this could be implemented in a standardized, reliable, and robust manner suitable for regulatory decision-making. Introduction of metabarcoding-based assessments of the soil microbiome into the PPP risk assessment would represent a significant increase in the degree of complexity of the data that needs to be processed and analyzed in comparison to the existing risk assessment on in-soil organisms. The bioinformatics procedures to process DNA sequences into community compositional data sets currently lack standardization, while little information exists on how these data should be used to generate regulatory endpoints and the ways in which these endpoints should be interpreted. Through a thorough and critical review, we explore these challenges. We conclude that currently, we do not have a sufficient degree of standardization or understanding of the required bioinformatics and data analysis procedures to consider their use in an environmental risk assessment context. However, we highlight critical knowledge gaps and the further research required to understand whether metabarcoding-based assessments of the soil microbiome can be utilized in a statistically and ecologically relevant manner within a PPP risk assessment. Only once these challenges are addressed can we consider if and how we should use metabarcoding as a tool for regulatory decision-making to assess and monitor ecotoxicological effects on soil microorganisms within an environmental risk assessment of PPPs. Integr Environ Assess Manag 2024;20:337-358. © 2023 SETAC.

Soil warming increases the number of growing bacterial taxa but not their growth rates

Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.

Experimental warming accelerates positive soil priming in a temperate grassland ecosystem

Unravelling biosphere feedback mechanisms is crucial for predicting the impacts of global warming. Soil priming, an effect of fresh plant-derived carbon (C) on native soil organic carbon (SOC) decomposition, is a key feedback mechanism that could release large amounts of soil C into the atmosphere. However, the impacts of climate warming on soil priming remain elusive. Here, we show that experimental warming accelerates soil priming by 12.7% in a temperate grassland. Warming alters bacterial communities, with 38% of unique active phylotypes detected under warming. The functional genes essential for soil C decomposition are also stimulated, which could be linked to priming effects. We incorporate lab-derived information into an ecosystem model showing that model parameter uncertainty can be reduced by 32-37%. Model simulations from 2010 to 2016 indicate an increase in soil C decomposition under warming, with a 9.1% rise in priming-induced CO2 emissions. If our findings can be generalized to other ecosystems over an extended period of time, soil priming could play an important role in terrestrial C cycle feedbacks and climate change.

Glucose input profit soil organic carbon mineralization and nitrogen dynamics in relation to nitrogen amended soils

Exogenous carbon (C) inputs stimulate soil organic carbon (SOC) decomposition, strongly influencing atmospheric concentrations and climate dynamics. The direction and magnitude of C decomposition depend on the C and nitrogen (N) addition, types and pattern. Despite the importance of decomposition, it remains unclear whether organic C input affects the SOC decomposition under different N-types (Ammonium Nitrate; AN, Urea; U and Ammonium Sulfate; AS). Therefore, we conducted an incubation experiment to assess glucose impact on N-treated soils at various levels (High N; HN: 50 mg/m2, Low N; LN: 05 mg/m2). The glucose input increased SOC mineralization by 38% and 35% under HN and LN, respectively. Moreover, it suppressed the concentration of NO3--N by 35% and NH4+-N by 15% in response to HN and LN soils, respectively. Results indicated higher respiration in Urea-treated soils and elevated net total nitrogen content (TN) in AS-treated soils. AN-amended soil exhibited no notable rise in C mineralization and TN content compared to other N-type soils. Microbial biomass carbon (MBC) was higher in glucose treated soils under LN conditions than control. This could result that high N suppressed microbial N mining and enhancing SOM stability by directing microbes towards accessible C sources. Our results suggest that glucose accelerated SOC mineralization in urea-added soils and TN contents in AS-amended soils, while HN levels suppressed C release and increased TN contents in all soil types except glucose-treated soils. Thus, different N-types and levels play a key role in modulating the stability of SOC over C input.

Carbon emissions and priming effects derived from crop residues and their responses to nitrogen inputs

Crop residue-derived carbon (C) emissions and priming effects (PE) in cropland soils can influence the global C cycle. However, their corresponding generality, driving factors, and responses to nitrogen (N) inputs are poorly understood. As a result, the total C emissions and net C balance also remain mysterious. To address the above knowledge gaps, a meta-analysis of 1123 observations, taken from 51 studies world-wide, has been completed. The results showed that within 360 days, emission ratios of crop residues C (ER) ranged from 0.22% to 61.80%, and crop residues generally induced positive PE (+71.76%). Comparatively, the contribution of crop residue-derived C emissions (52.82%) to total C emissions was generally higher than that of PE (12.08%), emphasizing the importance of reducing ER. The ER and PE differed among crop types, and both were low in the case of rice, which was attributed to its saturated water conditions. The ER and PE also varied with soil properties, as PE decreased with increasing C addition ratio in soils where soil organic carbon (SOC) was less than 10‰; in contrast, the opposite phenomenon was observed in soils with SOC exceeding 10‰. Moreover, N inputs increased ER and PE by 8.31% and 3.78%, respectively, which was predominantly attributed to (NH4 )2 SO4 . The increased PE was verified to be dominated by microbial stoichiometric decomposition. In summary, after incorporating crop residues, the total C emissions and relative net C balance in the cropland soils ranged from 0.03 to 23.47 mg C g-1 soil and 0.21 to 0.97 mg C g-1 residue-C g-1 soil, respectively, suggesting a significant impact on C cycle. These results clarify the value of incorporating crop residues into croplands to regulate global SOC dynamics and help to establish while managing site-specific crop return systems that facilitate C sequestration.

Shifts in bacterial traits under chronic nitrogen deposition align with soil processes in arbuscular, but not ectomycorrhizal-associated trees

Nitrogen (N) deposition increases soil carbon (C) storage by reducing microbial activity. These effects vary in soil beneath trees that associate with arbuscular (AM) and ectomycorrhizal (ECM) fungi. Variation in carbon C and N uptake traits among microbes may explain differences in soil nutrient cycling between mycorrhizal associations in response to high N loads, a mechanism not previously examined due to methodological limitations. Here, we used quantitative Stable Isotope Probing (qSIP) to measure bacterial C and N assimilation rates from an added organic compound, which we conceptualize as functional traits. As such, we applied a trait-based approach to explore whether variation in assimilation rates of bacterial taxa can inform shifts in soil function under chronic N deposition. We show taxon-specific and community-wide declines of bacterial C and N uptake under chronic N deposition in both AM and ECM soils. N deposition-induced reductions in microbial activity were mirrored by declines in soil organic matter mineralization rates in AM but not ECM soils. Our findings suggest C and N uptake traits of bacterial communities can predict C cycling feedbacks to N deposition in AM soils, but additional data, for instance on the traits of fungi, may be needed to connect microbial traits with soil C and N cycling in ECM systems. Our study also highlights the potential of employing qSIP in conjunction with trait-based analytical approaches to inform how ecological processes of microbial communities influence soil functioning.

Controls and significance of priming effects in lake sediments

Warming and eutrophication influence carbon (C) processing in sediments, with implications for the global greenhouse-gas budget. Temperature effects on sedimentary C loss are well understood, but the mechanism of change in turnover through priming with labile organic matter (OM) is not. Evaluating changes in the magnitude of priming as a function of warming, eutrophication, and OM stoichiometry, we incubated sediments with 13 C-labeled fresh organic matter (FOM, algal/cyanobacterial) and simulated future climate scenarios (+4°C and +8°C). We investigated FOM-induced production of CH4 and microbial community changes. C loss was primed by up to 17% in dominantly allochthonous sediments (ranging from 5% to 17%), compared to up to 6% in autochthonous sediments (-9% to 6%), suggesting that refractory OM is more susceptible to priming. The magnitude of priming was dependent on sediment OM stoichiometry (C/N ratio), the ratio of fresh labile OM to microbial biomass (FOM/MB), and temperature. Priming was strongest at 4°C when FOM/MB was below 50%. Addition of FOM was associated with activation and growth of bacterial decomposers, including for example, Firmicutes, Bacteroidetes, or Fibrobacteres, known for their potential to degrade insoluble and complex structural biopolymers. Using sedimentary C/N > 15 as a threshold, we show that in up to 35% of global lakes, sedimentation is dominated by allochthonous rather than autochthonous material. We then provide first-order estimates showing that, upon increase in phytoplankton biomass in these lakes, priming-enabled degradation of recalcitrant OM will release up to 2.1 Tg C annually, which would otherwise be buried for geological times.

Soil organic carbon priming co-regulated by labile carbon input level and long-term fertilization history

Labile carbon (C) input and fertilization have important consequences for soil organic matter (SOM) decomposition via the priming effect (PE), thereby impacting soil fertility and C sequestration. However, it remains largely uncertain on how the labile C input levels interact with long-term fertilization history to control PE intensity. To clarify this question, soil samples were collected from a 38-year fertilization field experiment (including five treatments: chemical nitrogen fertilizer, N; chemical fertilizer, NPK; manure, M1; 200 % manure, M2; NPK plus M2, NPKM2), with strongly altered soil physiochemical properties (i.e., soil aggregation, organic C and nutrient availability). These soil samples were incubated with three input levels of 13C-glucose (without glucose, control; low, 0.4 % SOC; high, 2.0 % SOC) to clarify the underlying mechanisms of PE. Results showed that the PE significantly increased with glucose input levels, with values increasing from negative or weak (-2.21 to 3.55 mg C g-1 SOC) at low input level to strongly positive (5.62 to 8.57 mg C g-1 SOC) at high input level across fertilization treatments. The increased PE intensity occurred along with decreased dissolved total nitrogen (DTN) contents and increased ratios of dissolved organic C to DTN, implying that the decline in N availability largely increased PE via enhanced microbial N mining from SOM. Compared to N and NPK treatments, the PE was significantly lower in the manure-amendment treatments, especially for low input level, due to more stable SOM by aggregate protection and higher N and phosphorus availability. These results suggested that manure application could alleviate SOM priming via increased soil C stability and nutrient availability. Collectively, our findings emphasize the importance of long-term fertilization-driven changes in labile C inputs, SOM stability, and nutrient availability in regulating PE and soil C dynamics. This knowledge advances our understanding of the long-term fertilization management for soil C sequestration.

Microbial controls over soil priming effects under chronic nitrogen and phosphorus additions in subtropical forests

The soil priming effect (PE), defined as the modification of soil organic matter decomposition by labile carbon (C) inputs, is known to influence C storage in terrestrial ecosystems. However, how chronic nutrient addition, particularly in leguminous and non-leguminous forests, will affect PE through interaction with nutrient (e.g., nitrogen and phosphorus) availability is still unclear. Therefore, we collected soils from leguminous and non-leguminous subtropical plantations across a suite of historical nutrient addition regimes. We added 13C-labeled glucose to investigate how background soil nutrient conditions and microbial communities affect priming and its potential microbial mechanisms. Glucose addition increased soil organic matter decomposition and prompted positive priming in all soils, regardless of dominant overstory tree species or fertilizer treatment. In non-leguminous soil, only combined nitrogen and phosphorus addition led to a higher positive priming than the control. Conversely, soils beneath N-fixing leguminous plants responded positively to P addition alone, as well as to joint NP addition compared to control. Using DNA stable-isotope probing, high-throughput quantitative PCR, enzyme assays and microbial C substrate utilization, we found that positive PE was associated with increased microbial C utilization, accompanied by an increase in microbial community activity, nutrient-related gene abundance, and enzyme activities. Our findings suggest that the balance between soil available N and P effects on the PE,  was dependent on rhizosphere microbial community composition. Furthermore, these findings highlight the roles of the interaction between plants and their symbiotic microbial communities in affecting soil priming and improve our understanding of the potential microbial pathways underlying soil PEs.

Resource partitioning and amino acid assimilation in a terrestrial geothermal spring

High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.

The contribution of wetland plant litter to soil carbon pool: Decomposition rates and priming effects

Plant litter input is an important driver of soil/sediment organic carbon (SOC) turnover. A large number of studies have targeted litter-derived C input tracing at a global level. However, little is known about how litter carbon (C) input via various plant tissues affects SOC accumulation and mineralization. Here, we conducted laboratory incubation to investigate the effects of leaf litter and stem litter input on SOC dynamics using the natural ¹³C isotope technique. A 122-day laboratory incubation period showed that litter input facilitated SOC accumulation. Leaf and stem litter inputs increased soil total organic carbon content by 37.6% and 15.5%, respectively. Leaf litter input had a higher contribution to SOC accumulation than stem litter input. Throughout the incubation period, the δ¹³C values of stem litter and leaf litter increased by 1.5‰ and 3.3‰, respectively, while δ¹³CO₂ derived from stem litter and δ¹³CO₂ derived from leaf litter decreased by 4.2‰ and 6.1‰, respectively, suggesting that the magnitude of δ¹³C in litter and δ¹³CO₂ shifts varied, depending on litter tissues. The cumulative CO₂-C emissions of leaf litter input treatments were 27.56%-42.47% higher than those of the stem litter input treatments, and thus leaf litter input promoted SOC mineralization more than stem litter input. Moreover, the proportion of increased CO₂-C emissions to cumulative CO₂-C emissions (57.18%-92.12%) was greater than the proportion of litter C input to total C (18.7%-36.8%), indicating that litter input could stimulate native SOC mineralization, which offsets litter-derived C in the soil. Overall, litter input caused a net increase in SOC accumulation, but it also accelerated the loss of native SOC. These findings provide a reliable basis for assessing SOC stability and net C sink capacity in wetlands.

Life history strategies among soil bacteria-dichotomy for few, continuum for many

Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both ¹⁸O-H₂O and ¹³C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms' joint ¹⁸O-¹³C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.

Nutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial community

Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, we analyze data from an experiment using quantitative stable isotope probing (qSIP) to estimate per-capita growth and mortality rates of bacterial populations in soils from several ecosystems along an elevation gradient which were subject to nutrient addition of either carbon alone (glucose; C) or carbon with nitrogen (glucose + ammonium-sulfate; C + N). Across all ecosystems, we found that higher population densities, quantified by the abundance of genomes per gram of soil, had lower per-capita growth rates in C + N-amended soils. Similarly, bacterial mortality rates in C + N-amended soils increased at a significantly higher rate with increasing population size than mortality rates in control and C-amended soils. In contrast to the hypothesis that density dependence would promote or maintain diversity, we observed significantly lower bacterial diversity in soils with stronger negative density-dependent growth. Here, density dependence was significantly but weakly responsive to nutrients and was not associated with higher bacterial diversity.

Vertical Distribution of Soil Bacterial Communities in Different Forest Types Along an Elevation Gradient

Microorganisms inhabit the entire soil profile and play important roles in nutrient cycling and soil formation. Recent studies have found that soil bacterial diversity and composition differ significantly among soil layers. However, little is known about the vertical variation in soil bacterial communities and how it may change along an elevation gradient. In this study, we collected soil samples from 5 forest types along an elevation gradient in Taibai Mountain to characterize the bacterial communities and their vertical patterns and variations across soil profiles. The richness and Shannon index of soil bacterial communities decreased from surface soils to deep soils in three forest types, and were comparable among soil layers in the other two forests at the medium elevation. The composition of soil bacterial communities differed significantly between soil layers in all forest types, and was primarily affected by soil C availability. Oligotrophic members of the bacterial taxa, such as Chloroflexi, Gemmatimonadetes, Nitrospirae, and AD3, were more abundant in the deep layers. The assembly of soil bacterial communities within each soil profile was mainly governed by deterministic processes based on environmental heterogeneity. The vertical variations in soil bacterial communities differed among forest types, and the soil bacterial communities in the Betula albo-sinensis forest at the medium elevation had the lowest vertical variation. The vertical variation was negatively correlated with mean annual precipitation (MAP), weighted rock content, and weighted sand particle content in soils, among which MAP had the highest explanatory power. These results indicated that the vertical mobilization of microbes with preferential and matrix flows likely enhanced bacterial homogeneity. Overall, our results suggest that the vertical variations in soil bacterial communities differ along the elevation gradient and potentially affect soil biological processes across soil profiles.

Elevated temperature and CO2 strongly affect the growth strategies of soil bacteria

The trait-based strategies of microorganisms appear to be phylogenetically conserved, but acclimation to climate change may complicate the scenario. To study the roles of phylogeny and environment on bacterial responses to sudden moisture increases, we determine bacterial population-specific growth rates by ¹⁸O-DNA quantitative stable isotope probing (¹⁸O-qSIP) in soils subjected to a free-air CO₂ enrichment (FACE) combined with warming. We find that three growth strategies of bacterial taxa - rapid, intermediate and slow responders, defined by the timing of the peak growth rates - are phylogenetically conserved, even at the sub-phylum level. For example, members of class Bacilli and Sphingobacteriia are mainly rapid responders. Climate regimes, however, modify the growth strategies of over 90% of species, partly confounding the initial phylogenetic pattern. The growth of rapid bacterial responders is more influenced by phylogeny, whereas the variance for slow responders is primarily explained by environmental conditions. Overall, these results highlight the role of phylogenetic and environmental constraints in understanding and predicting the growth strategies of soil microorganisms under global change scenarios.

Mechanisms underlying the succession of plant rhizosphere microbial community structure and function in an alpine open-pit coal mining disturbance zone

Elucidating the responses and potential functions of soil microbial communities during succession is important for understanding biogeochemical processes and the sustainable development of plant communities after environmental disturbances. However, studies of such dynamics during post-mining ecological restoration in alpine areas remain poorly understood. Microbial diversity, nitrogen, and phosphorus cycle functional gene potential in the Heishan mining area of Northwest China was studied, including primitive succession, secondary succession, and artificial succession disturbed by mining. The results revealed that: (1) The dominant bacteria in both categories (non-remediated and ecologically restored) of mining area rhizosphere soil were Proteobacteria, adopting the r strategy, whereas in naturally occurring soil outside the mining area, the dominant bacteria were actinomycetes and Acidobacteria, adopting the k strategy. Notably, mining perturbation significantly reduced the relative abundance of archaea. (2) After restoration, more bacterial network node connections were observed in mining areas than were originally present, whereas the archaeal network showed the opposite trend. (3) The networks of microbial genes related to nitrogen and phosphorus cycle potential differed significantly, depending on the succession type. Namely, prior to restoration, there were more phosphorus related functional gene network connections; these were also more strongly correlated, and the network was more aggregated. (4) Soil factors such as pH and NO₃-N affected both the mining area remediation soil and the soil outside the mining area, but did not affect the soil of the original vegetation in the mining area. The changes in the structure and function of plant rhizosphere microorganisms after mining disturbance can provide a theoretical basis for the natural restoration of mining areas.

Predicting the Postmortem Interval Based on Gravesoil Microbiome Data and a Random Forest Model

The estimation of a postmortem interval (PMI) is particularly important for forensic investigations. The aim of this study was to assess the succession of bacterial communities associated with the decomposition of mouse cadavers and determine the most important biomarker taxa for estimating PMIs. High-throughput sequencing was used to investigate the bacterial communities of gravesoil samples with different PMIs, and a random forest model was used to identify biomarker taxa. Redundancy analysis was used to determine the significance of environmental factors that were related to bacterial communities. Our data showed that the relative abundance of Proteobacteria, Bacteroidetes and Firmicutes showed an increasing trend during decomposition, but that of Acidobacteria, Actinobacteria and Chloroflexi decreased. At the genus level, Pseudomonas was the most abundant bacterial group, showing a trend similar to that of Proteobacteria. Soil temperature, total nitrogen, NH₄⁺-N and NO₃^--N levels were significantly related to the relative abundance of bacterial communities. Random forest models could predict PMIs with a mean absolute error of 1.27 days within 36 days of decomposition and identified 18 important biomarker taxa, such as Sphingobacterium, Solirubrobacter and Pseudomonas. Our results highlighted that microbiome data combined with machine learning algorithms could provide accurate models for predicting PMIs in forensic science and provide a better understanding of decomposition processes.

Particle size effects in microbial characteristics in thermophilic anaerobic digestion of cattle manure containing copper oxide

Roles of bulk-, micron-, and nano-copper oxide (CuO) on methane production, microbial diversity, functions during thermophilic anaerobic digestion (AD) were investigated in this study. Results showed that bulk-, micron-, and nano-CuO promoted methane production by 27.8%, 47.6%. and 83.1% compared to the control group, respectively. Microbial community analysis demonstrated that different particle sizes could cause various shifts on bacteria community, while had little effect on archaeal diversity. Thereinto, bacteria belonging to phylum Firmicutes and Coprothermobacterota dominated in enhanced hydrolysis process in groups with nano-CuO and bulk-CuO, respectively, while micron-CuO had stronger promotion on the abundances of hydrolytic and fermentative bacteria belonging to families Peptostreptococcaceae, Caloramatoraceae, Erysipelotrichaceae, and Clostridiaceae, than other two CuO sizes. Metabolic pathways revealed that energy-related metabolism and material transformation in bacteria were only boosted by micron-CuO, and nano-CuO and bulk-CuO were important to methanogenic activity, stimulating energy consumption and methane metabolism, respectively.

Partitioning of beta‐diversity reveals distinct assembly mechanisms of plant and soil microbial communities in response to nitrogen enrichment

Nitrogen (N) deposition poses a serious threat to terrestrial biodiversity and alters plant and soil microbial community composition. Species turnover and nestedness reflect the underlying mechanisms of variations in community composition. However, it remains unclear how species turnover and nestedness contribute to different responses of taxonomic groups (plants and soil microbes) to N enrichment. Here, based on a 13‐year consecutive multi‐level N addition experiment in a semiarid steppe, we partitioned community β‐diversity into species turnover and nestedness components and explored how and why plant and microbial communities reorganize via these two processes following N enrichment. We found that plant, soil bacterial, and fungal β‐diversity increased, but their two components showed different patterns with increasing N input. Plant β‐diversity was mainly driven by species turnover under lower N input but by nestedness under higher N input, which may be due to a reduction in forb species, with low tolerance to soil Mn²⁺, with increasing N input. However, turnover was the main contributor to differences in soil bacterial and fungal communities with increasing N input, indicating the phenomenon of microbial taxa replacement. The turnover of bacteria increased greatly whereas that of fungi remained within a narrow range with increasing N input. We further found that the increased soil Mn²⁺ concentration was the best predictor for increasing nestedness of plant communities under higher N input, whereas increasing N availability and acidification together contributed to the turnover of bacterial communities. However, environmental factors could explain neither fungal turnover nor nestedness. Our findings reflect two different pathways of community changes in plants, soil bacteria, and fungi, as well as their distinct community assembly in response to N enrichment. Disentangling the turnover and nestedness of plant and microbial β‐diversity would have important implications for understanding plant–soil microbe interactions and seeking conservation strategies for maintaining regional diversity.

Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana

The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments.

Soil minerals affect taxon-specific bacterial growth

Secondary minerals (clays and metal oxides) are important components of the soil matrix. Clay minerals affect soil carbon persistence and cycling, and they also select for distinct microbial communities. Here we show that soil mineral assemblages-particularly short-range order minerals-affect both bacterial community composition and taxon-specific growth. Three soils with different parent material and presence of short-range order minerals were collected from ecosystems with similar vegetation and climate. These three soils were provided with ¹⁸O-labeled water and incubated with or without artificial root exudates or pine needle litter. Quantitative stable isotope probing was used to determine taxon-specific growth. We found that the growth of bacteria varied among soils of different mineral assemblages but found the trend of growth suppression in the presence of short-range order minerals. Relative growth of bacteria declined with increasing concentration of short-range order minerals between 25-36% of taxa present in all soils. Carbon addition in the form of plant litter or root exudates weakly affected relative growth of taxa (p = 0.09) compared to the soil type (p < 0.01). However, both exudate and litter carbon stimulated growth for at least 34% of families in the soils with the most and least short-range order minerals. In the intermediate short-range order soil, fresh carbon reduced growth for more bacterial families than were stimulated. These results highlight how bacterial-mineral-substrate interactions are critical to soil organic carbon processing, and how growth variation in bacterial taxa in these interactions may contribute to soil carbon persistence and loss.

Variation in Soil Bacterial and Fungal Community Composition at Different Successional Stages of a Broad-Leaved Korean Pine Forest in the Lesser Hinggan Mountains

Soil microorganisms are an integral part of the soil and are highly sensitive to environmental changes. The shift in plant community and soil properties following forest succession may cause differences in soil bacterial and fungal community composition. Some studies suggested following the succession of the community, the species composition tends to switch from r-strategy groups to k-strategy groups. However, generalization on the changing pattern has not been worked out. Three forests at an early-, intermediate-, and late-stage (ES, IS, LS) of the succession of broad-leaved Korean pine forest in the Lesser Hinggan Mountains were surveyed to study the variation in soil bacterial and fungal community composition as the succession proceeds. Soil microbial community composition and related soil factors were analyzed by systematic sampling. Significant differences in soil microbial community composition were detected between forests at different stages. The bacterial diversity increased, while the fungal diversity decreased (p < 0.05) from the early to the late successional forest. The fungi to bacteria ratio (F/B) and the (Proteobacteria + Bacteroidetes) to (Actinobacteria + Acidobacteria) ratio increased substantially with succession (p < 0.05). At the phylum level, Bacteroidetes, Ascomycota and Mortierellomycota were dominant in the ES forest, while Actinobacteria and Basidiomycota were prevalent in the LS forest. At the class level, Gammaproteobacteria, Acidobacteriia, Bacteroidia, Sordariomycetes and Mortierellomycetes were dominant in the ES forest, whereas Subgroup_6, Agaricomycetes, Geminibasidiomycetes and Tremellomycetes were dominant in the LS forest. Soil water content (SWC) and available phosphorus (AP) had significant effects on the bacterial community composition (p < 0.05). Soil organic carbon (SOC), total nitrogen (TN), the carbon–nitrogen ratio (C/N), total potassium (TK) and SWC had significant effects on the fungal community composition (p < 0.05). SOC and TN were positively correlated with r-strategy groups (p < 0.05) and were significantly negatively correlated with k-strategy groups (p < 0.05). Our results suggest that the soil bacterial and fungal community composition changed significantly in forests across the successional stages, and the species composition switched from r-strategy to k-strategy groups. The bacterial and fungal community diversity variation differed in forests across the successional stages. The changes in soil organic carbon and nitrogen content resulted in the shifting of microbial species with different ecological strategies.

Phylogenetic organization in the assimilation of chemically distinct substrates by soil bacteria

Soils are among the most biodiverse habitats on earth and while the species composition of microbial communities can influence decomposition rates and pathways, the functional significance of many microbial species and phylogenetic groups remains unknown. If bacteria exhibit phylogenetic organization in their function, this could enable ecologically meaningful classification of bacterial clades. Here, we show non-random phylogenetic organization in the rates of relative carbon assimilation for both rapidly mineralized substrates (amino acids and glucose) assimilated by many microbial taxa and slowly mineralized substrates (lipids and cellulose) assimilated by relatively few microbial taxa. When mapped onto bacterial phylogeny using ancestral character estimation this phylogenetic organization enabled the identification of clades involved in the decomposition of specific soil organic matter substrates. Phylogenetic organization in substrate assimilation could provide a basis for predicting the functional attributes of uncharacterized microbial taxa and understanding the significance of microbial community composition for soil organic matter decomposition.

Perna canaliculus as an Ecological Material in the Removal of o-Cresol Pollutants from Soil

Soil contamination with cresol is a problem of the 21st century and poses a threat to soil microorganisms, humans, animals, and plants. The lack of precise data on the potential toxicity of o-cresol in soil microbiome and biochemical activity, as well as the search for effective remediation methods, inspired the aim of this study. Soil is subjected to four levels of contamination with o-cresol: 0, 0.1, 1, 10, and 50 mg o-cresol kg-1 dry matter (DM) of soil and the following are determined: the count of eight groups of microorganisms, colony development index (CD) and ecophysiological diversity index (EP) for organotrophic bacteria, actinobacteria and fungi, and the bacterial genetic diversity. Moreover, the responses of seven soil enzymes are investigated. Perna canaliculus is a recognized biosorbent of organic pollutants. Therefore, microbial biostimulation with Perna canaliculus shells is used to eliminate the negative effect of the phenolic compound on the soil microbiome. Fungi appears to be the microorganisms most sensitive to o-cresol, while Pseudomonas sp. is the least sensitive. In o-cresol-contaminated soils, the microbiome is represented mainly by the bacteria of the Proteobacteria and Firmicutes phyla. Acid phosphatase, alkaline phosphatase and urease can be regarded as sensitive indicators of soil disturbance. Perna canaliculus shells prove to be an effective biostimulator of soil under pressure with o-cresol.

Sugar and organic acid availability modulate soil diazotroph community assembly and species co-occurrence patterns on the Tibetan Plateau

Metabolites can mediate species interactions and the assembly of microbial communities. However, how these chemicals relate to the assembly processes and co-occurrence patterns of diazotrophic assemblages in root-associated soils remains largely unknown. Here, we examined the diversity and assembly of diazotrophic communities and further deciphered their links with metabolites on Tibetan Plateau. We found that the distribution of sugars and organic acids in the root-associated soils was significantly correlated with the richness of diazotrophs. The presence of these two soil metabolites explains the variability in diazotrophic community compositions. The differential concentrations of these metabolites were significantly linked with the distinctive abundances of diazotrophic taxa in same land types dominated by different plants or dissimilar soils by same plants. The assembly of diazotrophic communities is subject to deterministic ecological processes, which are widely modulated by the variety and amount of sugars and organic acids. Organic acids, for instance, 3-(4-hydroxyphenyl)propionic acid and citric acid, were effective predictors of the characteristics of diazotrophic assemblages across desert habitats. Diazotrophic co-occurrence networks tended to be more complex and connected within different land types covered by the same plant species. The concentrations of multiple sugars and organic acids were coupled significantly with the distribution of keystone species, such as Azotobacter, Azospirillum, Bradyrhizobium, and Mesorhizobium, in the co-occurrence network. These findings provide new insights into the assembly mechanisms of root-associated diazotrophic communities across the desert ecosystems of the Tibetan Plateau.Key points• Soil metabolites were significantly linked to the diversity of diazotrophic community.• Soil metabolites determined the assembly of diazotrophic community.• Sugars and organic acids were coupled mainly with keystone species in networks.

Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil

Microbial decomposition drives the transformation of plant-derived substrates into microbial products that form stable soil organic matter (SOM). Recent theories have posited that decomposition depends on an interaction between SOM chemistry with microbial diversity and resulting function (e.g., enzymatic capabilities, growth rates). Here, we explicitly test these theories by coupling quantitative stable isotope probing and metabolomics to track the fate of ¹³C enriched substrates that vary in chemical composition as they are assimilated by microbes and transformed into new metabolic products in soil. We found that differences in forest nutrient economies (e.g., nutrient cycling, microbial competition) led to arbuscular mycorrhizal (AM) soils harboring greater diversity of fungi and bacteria than ectomycorrhizal (ECM) soils. When incubated with ¹³C enriched substrates, substrate type drove shifts in which species were active decomposers and the abundance of metabolic products that were reduced or saturated in the highly diverse AM soils. The decomposition pathways were more static in the less diverse, ECM soil. Importantly, the majority of these shifts were driven by taxa only present in the AM soil suggesting a strong link between microbial identity and their ability to decompose and assimilate substrates. Collectively, these results highlight an important interaction between ecosystem-level processes and microbial diversity; whereby the identity and function of active decomposers impacts the composition of decomposition products that can form stable SOM.

Soil pH and Organic Carbon Properties Drive Soil Bacterial Communities in Surface and Deep Layers Along an Elevational Gradient

Elevational gradients strongly affect the spatial distribution and structure of soil bacterial communities. However, our understanding of the effects and determining factors is still limited, especially in the deep soil layer. Here, we investigated the diversity and composition of soil bacterial communities in different soil layers along a 1,500-m elevational gradient in the Taibai Mountain. The variables associated with climate conditions, plant communities, and soil properties were analyzed to assess their contributions to the variations in bacterial communities. Soil bacterial richness and α-diversity showed a hump-shaped trend with elevation in both surface and deep layers. In the surface layer, pH was the main factor driving the elevational pattern in bacterial diversity, while in the deep layer, pH and soil carbon (C) availability were the two main predictors. Bacterial community composition differed significantly along the elevational gradient in all soil layers. In the surface layer, Acidobacteria, Delta-proteobacteria, and Planctomycetes were significantly more abundant in the lower elevation sites than in the higher elevation sites; and Gemmatimonadetes, Chloroflexi, and Beta-proteobacteria were more abundant in the higher elevation sites. In the deep layer, AD3 was most abundant in the highest elevation site. The elevational pattern of community composition co-varied with mean annual temperature, mean annual precipitation, diversity and basal area of trees, pH, soil C availability, and soil C fractions. Statistical results showed that pH was the main driver of the elevational pattern of the bacterial community composition in the surface soil layer, while soil C fractions contributed more to the variance of the bacterial composition in the deep soil layer. These results indicated that changes in soil bacterial communities along the elevational gradient were driven by soil properties in both surface and deep soil layers, which are critical for predicting ecosystem functions under future climate change scenarios.

Nutrients cause consolidation of soil carbon flux to small proportion of bacterial community

Nutrient amendment diminished bacterial functional diversity, consolidating carbon flow through fewer bacterial taxa. Here, we show strong differences in the bacterial taxa responsible for respiration from four ecosystems, indicating the potential for taxon-specific control over soil carbon cycling. Trends in functional diversity, defined as the richness of bacteria contributing to carbon flux and their equitability of carbon use, paralleled trends in taxonomic diversity although functional diversity was lower overall. Among genera common to all ecosystems, Bradyrhizobium, the Acidobacteria genus RB41, and Streptomyces together composed 45–57% of carbon flow through bacterial productivity and respiration. Bacteria that utilized the most carbon amendment (glucose) were also those that utilized the most native soil carbon, suggesting that the behavior of key soil taxa may influence carbon balance. Mapping carbon flow through different microbial taxa as demonstrated here is crucial in developing taxon-sensitive soil carbon models that may reduce the uncertainty in climate change projections.

The fate of soil carbon depends on microbial processes, but whether different microbial taxa have individualistic effects on carbon fluxes is unknown. Here the authors use 16 S amplicon sequencing and stable isotopes to show how taxonomic differences influence bacterial respiration and carbon cycling across four ecosystems.

Microbial species performance responses to environmental changes: genomic traits and nutrient availability

How microbial species performance indicators, such as growth rate and carbon assimilation rate, respond to environmental changes is a challenging question, especially for complex communities. This limits our ability to understand how species performance responses to environmental changes (that is, species environmental responses) of microbes could be linked to genomic traits and nutrient availability. Based on stable isotope labeling of DNA, we propose a new approach with effect-size metrics to quantify the species environmental responses of microbes by comparing the species performance between defined control and treatment groups. The species performance within microbial communities of the natural or altered environments could be quantitatively determined with quantitative stable isotope probing (qSIP). We further apply this approach, namely effect-size qSIP, to measure species environmental responses upon carbon and nitrogen additions for soil bacteria on mountainsides and to understand their responses from the perspective of genomic traits. Towards high elevations, there is a stronger nitrogen limitation that is indicated by the higher aggregated responses, measured as community-weighted means, of bacterial growth rate upon nitrogen additions. The aggregated responses are further explained by genomic traits, which show higher percentages of significant Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues (KOs) and more diverse KEGG pathways under nutrient additions including nitrogen, and further improve the explanatory power of microbial environmental responses. Nitrogen-induced responses at the species level show the strongest associations with essential KOs for rare species, whereas carbon-induced responses show the strongest associations for dominant species. We conclude that, in addition to environmental determinants such as nitrogen limitation, genomic traits are extremely important for predicting microbial environmental responses at both the community and species levels. Taking advantage of this new approach at the species level, we reveal that rare and dominant species differentially respond to nutrient enrichment via their metabolic traits. The approach and findings can lead to a more holistic understanding of microbial environmental responses in natural habitats, which will be essential for predicting microbial community responses to global environmental changes.

The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization

Microorganisms drive soil carbon mineralization and changes in their activity with increased temperature could feedback to climate change. Variation in microbial biodiversity and the temperature sensitivities (Q₁₀) of individual taxa may explain differences in the Q₁₀ of soil respiration, a possibility not previously examined due to methodological limitations. Here, we show phylogenetic and taxonomic variation in the Q₁₀ of growth (5-35 °C) among soil bacteria from four sites, one from each of Arctic, boreal, temperate, and tropical biomes. Differences in the temperature sensitivities of taxa and the taxonomic composition of communities determined community-assembled bacterial growth Q₁₀, which was strongly predictive of soil respiration Q₁₀ within and across biomes. Our results suggest community-assembled traits of microbial taxa may enable enhanced prediction of carbon cycling feedbacks to climate change in ecosystems across the globe.

Phenolic acid-degrading Paraburkholderia prime decomposition in forest soil

Plant-derived phenolic acids are catabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria enhance SOC mineralization in forest soils when primed with 13C-labeled p-hydroxybenzoic acid (pHB). We further tested whether pHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. pHB addition primed significant losses of SOC (3-13 µmols C g-1 dry wt soil over 7 days) compared to glucose, which reduced mineralization (-3 to -8 µmols C g-1 dry wt soil over 7 days). The principal degraders of pHB were Paraburkholderia and Caballeronia in all plantations regardless of tree species or soil type, with one predominant phylotype (RP11ASV) enriched 23-fold following peak pHB respiration. We isolated and confirmed the phenolic degrading activity of a strain matching this phylotype (RP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, Dyp-type peroxidase and aryl-alcohol oxidase. Increased relative abundance of RP11ASV corresponded with higher pHB respiration and expression of pHB monooxygenase (pobA), which was inversely proportional to SOC content among plantations. pobA expression proved a responsive measure of priming activity. We found that stimulating phenolic-acid degrading bacteria can prime decomposition and that this activity, corresponding with differences in tree species, is a potential mechanism in SOC cycling in forests. Overall, this study highlights the ecology and function of Paraburkholderia whose associations with plant roots and capacity to degrade phenolics suggest a role for specialized bacteria in the priming effect.

Microbes changed their carbon use strategy to regulate the priming effect in an 11-year nitrogen addition experiment in grassland

Nitrogen availability is a key factor that regulates soil priming (the strong short-term changes in microbial decomposition of soil organic carbon after addition of fresh carbon resources); however, how soil priming changes under nitrogen addition is unclear. In this study, we collected soils from a grassland with 11-year history of nitrogen addition (0, 60, 120, and 240 kg N ha^-1 yr^-1 NH₄NO₃), and the soils were incubated for 6 weeks to estimate the direction and magnitude of soil priming and the underlying microbial carbon use strategy. We found glucose addition triggered a positive priming effect among all the treatments; however, the magnitude of the positive priming did not change under nitrogen addition. The stable soil organic carbon content under different nitrogen addition levels might support the no significant change in the magnitude of those positive priming. Using DNA stable-isotope probing (DNA-SIP), we found that bacterial and fungal taxa consuming the added glucose were different in different nitrogen addition levels. The relative abundance of the K-strategist Acidobacteria increased with increasing nitrogen addition levels, while the r-strategist Firmicutes decreased with increasing nitrogen addition levels. Our results indicated microbial taxa exhibited carbon use plasticity, with most taxa altering their use of glucose under nitrogen addition.

Rhizosphere effects on soil microbial community structure and enzyme activity in a successional subtropical forest

Forest succession is a central ecological topic due to the importance of its dynamic process for terrestrial ecosystems. However, we have limited knowledge of the relationship between forest succession and belowground microbiota, particularly regarding interactions in the rhizosphere. Here, we determined microbial community structure and biomass using phospholipid fatty acid (PLFA) biomarkers and microbial activity using extracellular enzyme activity in bulk and rhizosphere soils from three successional stages of subtropical forests in eastern China. Principal component analysis of PLFAs indicated distinct soil microbial communities among different successional stages and habitat locations. Specifically for the topsoil, we found the total microbial biomass, bacterial biomass and enzyme activities showed higher levels in the late than early stage, with a significant succession-induced accentuated rhizosphere effect. The increase in total microbial biomass and activity coincided with a net growth in bacterial rather than fungal biomass, indicating a model in which microbial biomass carrying capacity and activity could be affected by the creation or expansion of niches for certain functional group rather than by a rebalancing of competitive interactions among these groups. Furthermore, we demonstrated that forest succession significantly influenced enzyme activity via the changes in microbial biomass, as driven by edaphic factors. Overall, our study deepens the mechanistic understanding of forest recovery by linking soil microbial community and activity along successional chronosequences.

Glucose triggers strong taxon-specific responses in microbial growth and activity: insights from DNA and RNA qSIP

Growth of soil microorganisms is often described as carbon limited, and adding labile carbon to soil often results in a transient and large increase in respiration. In contrast, soil microbial biomass changes little, suggesting that growth and respiration are decoupled in response to a carbon pulse. Alternatively, measuring bulk responses of the entire community (total respiration and biomass) could mask ecologically important variation among taxa in response to the added carbon. Here, we assessed taxon-specific variation in cellular growth (measured as DNA synthesis) and metabolic activity (measured as rRNA synthesis) following glucose addition to soil using quantitative stable isotope probing with H₂ ¹⁸ O. We found that glucose addition altered rates of DNA and rRNA synthesis, but the effects were strongly taxon specific: glucose stimulated growth and rRNA transcription for some taxa, and suppressed these for others. These contrasting taxon-specific responses could explain the small and transient changes in total soil microbial biomass. Responses to glucose were not well predicted by a priori assignments of taxa into copiotrophic or oligotrophic categories. Across all taxa, rates of DNA and rRNA synthesis changed in parallel, indicating that growth and activity were coupled, and the degree of coupling was unaffected by glucose addition. This pattern argues against the idea that labile carbon addition causes a large reduction in metabolic growth efficiency; rather, the large pulse of respiration observed with labile substrate addition is more likely to be the result of rapid turnover of microbial biomass, possibly due to trophic interactions. Our results support a strong connection between rRNA synthesis and bacterial growth, and indicate that taxon-specific responses among soil bacteria can buffer responses at the scale of the whole community.

Microbial carbon use efficiency predicted from genome-scale metabolic models

Respiration by soil bacteria and fungi is one of the largest fluxes of carbon (C) from the land surface. Although this flux is a direct product of microbial metabolism, controls over metabolism and their responses to global change are a major uncertainty in the global C cycle. Here, we explore an in silico approach to predict bacterial C-use efficiency (CUE) for over 200 species using genome-specific constraint-based metabolic modeling. We find that potential CUE averages 0.62 ± 0.17 with a range of 0.22 to 0.98 across taxa and phylogenetic structuring at the subphylum levels. Potential CUE is negatively correlated with genome size, while taxa with larger genomes are able to access a wider variety of C substrates. Incorporating the range of CUE values reported here into a next-generation model of soil biogeochemistry suggests that these differences in physiology across microbial taxa can feed back on soil-C cycling.

Global ecological predictors of the soil priming effect

Identifying the global drivers of soil priming is essential to understanding C cycling in terrestrial ecosystems. We conducted a survey of soils across 86 globally-distributed locations, spanning a wide range of climates, biotic communities, and soil conditions, and evaluated the apparent soil priming effect using ¹³C-glucose labeling. Here we show that the magnitude of the positive apparent priming effect (increase in CO₂ release through accelerated microbial biomass turnover) was negatively associated with SOC content and microbial respiration rates. Our statistical modeling suggests that apparent priming effects tend to be negative in more mesic sites associated with higher SOC contents. In contrast, a single-input of labile C causes positive apparent priming effects in more arid locations with low SOC contents. Our results provide solid evidence that SOC content plays a critical role in regulating apparent priming effects, with important implications for the improvement of C cycling models under global change scenarios.

The global ecological predictors of soil priming remain unclear. Here the authors conducted a global survey of soils from 86 global locations using an isotopic approach and find that in more mesic sites with high SOC concentrations, soil priming effects are more likely to be negative.

Predictive genomic traits for bacterial growth in culture versus actual growth in soil

Relationships between microbial genes and performance are often evaluated in the laboratory in pure cultures, with little validation in nature. Here, we show that genomic traits related to laboratory measurements of maximum growth potential failed to predict the growth rates of bacteria in unamended soil, but successfully predicted growth responses to resource pulses: growth increased with 16S rRNA gene copy number and declined with genome size after substrate addition to soils, responses that were repeated in four different ecosystems. Genome size best predicted growth rate in response to addition of glucose alone; adding ammonium with glucose weakened the relationship, and the relationship was absent in nutrient-replete pure cultures, consistent with the idea that reduced genome size is a mechanism of nutrient conservation. Our findings demonstrate that genomic traits of soil bacteria can map to their ecological performance in nature, but the mapping is poor under native soil conditions, where genomic traits related to stress tolerance may prove more predictive. These results remind that phenotype depends on environmental context, underscoring the importance of verifying proposed schemes of trait-based strategies through direct measurement of performance in nature, an important and currently missing foundation for translating microbial processes from genes to ecosystems.

Predictive genomic traits for bacterial growth in culture versus actual growth in soil

Relationships between microbial genes and performance are often evaluated in the laboratory in pure cultures, with little validation in nature. Here, we show that genomic traits related to laboratory measurements of maximum growth potential failed to predict the growth rates of bacteria in unamended soil, but successfully predicted growth responses to resource pulses: growth increased with 16S rRNA gene copy number and declined with genome size after substrate addition to soils, responses that were repeated in four different ecosystems. Genome size best predicted growth rate in response to addition of glucose alone; adding ammonium with glucose weakened the relationship, and the relationship was absent in nutrient-replete pure cultures, consistent with the idea that reduced genome size is a mechanism of nutrient conservation. Our findings demonstrate that genomic traits of soil bacteria can map to their ecological performance in nature, but the mapping is poor under native soil conditions, where genomic traits related to stress tolerance may prove more predictive. These results remind that phenotype depends on environmental context, underscoring the importance of verifying proposed schemes of trait-based strategies through direct measurement of performance in nature, an important and currently missing foundation for translating microbial processes from genes to ecosystems.

Susceptibility of soil organic carbon to priming after long-term CO2 fumigation is mediated by soil texture

Elevated CO₂ (eCO₂) may enhance soil organic carbon (SOC) sequestration via greater input of photosynthetic carbon (C). However, greater rhizodeposits under eCO₂ may stimulate microbial decomposition of native SOC. This study aimed to examine the status and stability of SOC in three Australian cropping soils after long-term CO₂ enrichment. Samples (0-5 cm) of Chromosol, Vertosol and Calcarosol soils were collected from an 8-year Free-air CO₂ Enrichment (SoilFACE) experiment and were used to examine SOC dynamics by physical fractionation and incubation with ¹³C-glucose. Compared to the ambient CO₂ (aCO₂) (390-400 μmol mol^-1), 8 years of elevated CO₂ (eCO₂) (550 μmol mol^-1) did not increase SOC concentration of all soils, but changed SOC distribution with 12% more C in coarse soil fractions and 5% less C in fine fractions. Elevated CO₂ also enhanced the susceptibility of SOC to ¹³C-glucose-induced priming, but this effect was only significant in the coarse-textured Calcarosol topsoil. The eCO₂ history increased labile C (coarse C fraction, +13%) and soil pH (+0.25 units), and decreased available N (-30%) in the Calcarosol, which stimulated microbial biomass C by 28%, leading to an enhanced priming effect. Despite with greater total primed C, the Chromosol that had the highest amount of native C, had lower primed C per unit of SOC when compared to the low-C Calcarosol. In conclusion, the effect of long-term eCO₂ enrichment on soil C and N availability in cropping soils depended on soil type with the coarse-textured Calcarosol soil being more susceptible to substrate-induced decomposition of its SOC.

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H₂¹⁸O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), ¹⁸O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. ¹⁸O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became ¹⁸O labeled only during euxinic conditions. Sequencing of these ¹⁸O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of "microbial dark matter", validating hypotheses put forth by earlier metagenomic studies.

Seasonal, sub-seasonal and diurnal variation of soil bacterial community composition in a temperate deciduous forest

The temporal dynamics of soil bacterial communities are understudied, but such understanding is critical to elucidating the drivers of community variation. The goal of this study was to characterize how soil bacterial communities vary across diurnal, sub-seasonal and seasonal time-scales in a 5.8 m2 plot and test the hypothesis that bacterial diversity varies on each of these scales. We used 16S rDNA gene amplicon sequencing to quantify the alpha and beta diversity of soil bacteria as well as the Net Relatedness Index and Nearest Taxon Indices to assess the degree of phylogenetic clustering, and the extent to which community shifts were driven by stochastic vs. deterministic limitation. We found that species richness was highest in winter, lowest in fall and that communities were compositionally distinct across seasons. There was no evidence of diurnal-scale shifts; the finest temporal scale over which community shifts were detected using our DNA-based analysis was between sampling dates separated by 6 weeks. Phylogenetic analyses suggested that seasonal-scale differences in community composition were the result of environmental filtering and homogeneous selection. Our findings provide insight into temporal variation of soil bacterial communities across the hourly to seasonal scales while minimizing the potential confounding effect of spatial variation.

Environmental filtering drives bacterial community structure and function in a subalpine area of northern China

Microbial community assembly is affected by the trade-off between deterministic and stochastic processes, but the mechanisms underpinning their relative influences remain elusive. This knowledge gap strongly limits our ability to predict the effect of environmental filtering on microbial community structure and function. To improve the understanding of mechanisms underlying community assembly processes, we investigated bacterial community structure and function on a subalpine shady slope and a sunny slope in the Pangquangou National Nature Reserve in North China. By integrating the results of a null model and the RC metric, we inferred that a deterministic process, that is, environmental filtering, drove bacterial community biogeographical patterns. Edaphic factors caused the largest contribution to microbial community structure, followed by vegetation and spatial variables. Among edaphic factors, total carbon (TC) and total nitrogen (TN) were the most important factors as determined by redundancy analysis (RDA). Moreover, network analysis suggested that the status of bacterial community co-occurrence was significantly greater than that of exclusive relationships. Under environmental stress, there was no significant difference in the overall bacterial community structure on the different slopes, while significant differences were observed in relation to community functions. Given this, we inferred that the degrees of response of bacterial community structure and function to varying environments were not consistent. In conclusion, our results contribute to the understanding of deterministic versus stochastic balance in bacterial community assembly and the response mechanisms of community structure and function to environmental heterogeneity.

Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing

Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ “dark” primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover.

Benthic environments harbor highly diverse and complex microbial communities that control carbon fluxes, but the role of specific uncultivated microbial groups in organic matter turnover is poorly understood. In this study, quantitative DNA stable isotope probing (DNA-qSIP) was used for the first time to link uncultivated populations of bacteria and archaea to carbon turnover in lacustrine surface sediments. After 1-week incubations in the dark with [¹³C]bicarbonate, DNA-qSIP showed that ammonia-oxidizing archaea (AOA) were the dominant active chemolithoautotrophs involved in the production of new organic matter. Natural ¹³C-labeled organic matter was then obtained by incubating sediments in the dark for 2.5 months with [¹³C]bicarbonate, followed by extraction and concentration of high-molecular-weight (HMW) (>50-kDa) organic matter. qSIP showed that the labeled organic matter was turned over within 1 week by 823 microbial populations (operational taxonomic units [OTUs]) affiliated primarily with heterotrophic Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes. However, several OTUs affiliated with the candidate microbial taxa Latescibacteria, Omnitrophica, Aminicentantes, Cloacimonates, AC1, Bathyarchaeota, and Woesearchaeota, groups known only from genomic signatures, also contributed to biomass turnover. Of these 823 labeled OTUs, 52% (primarily affiliated with Proteobacteria) also became labeled in 1-week incubations with [¹³C]bicarbonate, indicating that they turned over carbon faster than OTUs that were labeled only in incubations with ¹³C-labeled HMW organic matter. These taxa consisted primarily of uncultivated populations within the Firmicutes, Bacteroidetes, Verrucomicrobia, and Chloroflexi, highlighting their ecological importance. Our study helps define the role of several poorly understood, uncultivated microbial groups in the turnover of benthic carbon derived from “dark” primary production.

IMPORTANCE Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ “dark” primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover.

Global effects of plant litter alterations on soil CO2 to the atmosphere

Soil respiration (Rs) is the largest terrestrial carbon (C) efflux to the atmosphere and is predicted to increase drastically through global warming. However, the responses of Rs to global warming are complicated by the fact that terrestrial plant growth and the subsequent input of plant litter to soil are also altered by ongoing climate change and human activities. Despite a number of experiments established in various ecosystems around the world, it remains a challenge to predict the magnitude and direction of changes in Rs and its temperature sensitivity (Q₁₀ ) due to litter alteration. We present a meta-analysis of 100 published studies to examine the responses of Rs and Q₁₀ to manipulated aboveground and belowground litter alterations. We found that 100% aboveground litter addition (double litter) increased Rs by 26.1% (95% confident intervals, 18.4%-33.7%), whereas 100% aboveground litter removal, root removal and litter + root removal reduced Rs by 22.8% (18.5%-27.1%), 34.1% (27.2%-40.9%) and 43.4% (36.6%-50.2%) respectively. Moreover, the effects of aboveground double litter and litter removal on Rs increased with experimental duration, but not those of root removal. Aboveground litter removal marginally increased Q₁₀ by 6.2% (0.2%-12.3%) because of the higher temperature sensitivity of stable C substrate than fresh litter. Estimated from the studies that simultaneously tested the responses of Rs to aboveground litter addition and removal and assuming negligible changes in root-derived Rs, "priming effect" on average accounted for 7.3% (0.6%-14.0%) of Rs and increased over time. Across the global variation in terrestrial ecosystems, the effects of aboveground litter removal, root removal, litter + root removal on Rs as well as the positive effect of litter removal on Q₁₀ increased with water availability. Our meta-analysis indicates that priming effects should be considered in predicting Rs to climate change-induced increases in litterfall. Our analysis also highlights the need to incorporate spatial climate gradient in projecting long-term Rs responses to litter alterations.

The effect of biochar feedstock, pyrolysis temperature, and application rate on the reduction of ammonia volatilisation from biochar-amended soil

Ammonia (NH₃) volatilisation is one of the most important causes of nitrogen (N) loss in soil-plant systems worldwide. Carbon-based amendments such as biochar have been shown to mitigate NH₃ volatilisation in agricultural soils to various degrees. In this study, we investigated the influence of biochar feedstocks (poultry manure, green waste compost, and wheat straw), pyrolysis temperatures (250, 350, 450, 500 and 700°C) and application rates (1 and 2%), on NH₃ volatilisation from a calcareous soil. The 15 biochars were chemically characterized, and a laboratory incubation study was conducted to assess NH₃ volatilisation from the soil over a period of four weeks. Furthermore, changes to the bacterial and fungal communities were assessed via sequencing of phylogenetic marker genes. The study showed that biochar feedstock sources, pyrolysis temperature, and application rates all affected NH₃ volatilisation. Overall, low pyrolysis temperature biochars and higher biochar application rates achieved greater reductions in NH₃ volatilisation. A feedstock related effect was also observed, with poultry manure biochar reducing NH₃ volatilisation by an average of 53% in comparison to 38% and 35% reductions for biochar from green waste compost and wheat straw respectively. Results indicate that the biogeochemistry underlying biochar-mediated reduction in NH₃ volatilisation is complex and caused by changes in soil pH, NH₃ sorption and microbial community composition (especially ammonia oxidising guilds).