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This paper shows that CH4 produced in the heartwood of living trees in upland forests is of microbial origin, and that microbial CH4 production may be suppressed in the heartwood with more phenolic compounds than carbohydrates. Methane (CH4) is a potent greenhouse gas that exerts large effects on atmospheric chemistry and the global warming. Living trees in upland forests might contribute to the global CH4 emissions but the contribution is poorly understood and the mechanisms of CH4 production in their heartwood are not completely clear. Using gene sequencing and a series of laboratory incubations, this study addressed whether CH4 produced in the heartwood of living trees in upland forests is microbial in origin and how the CH4 production is affected by secondary metabolites. Both the response of CH4 production to temperatures and the presence of methanogenic archaea indicate that the CH4 produced in heartwood was microbial in origin. Methanobacterium was the dominant methanogens in the heartwood of Populus canadensis which had high concentrations of CH4, and was absent from the heartwood of Pinus tabuliformis and Salix matsudana which produced negligible or very low CH4. Water- and ethanol-soluble extractives enhanced microbial CH4 production in heartwood incubations but acetone-soluble extractives inhibited the production. Since acetone-soluble extractives inhibited the production of microbial CH4, it is assumed that the CH4 production may be suppressed from heartwood with phenolic compounds that act as an antibiotic for methanogenic archaea in most living trees in upland forests. The inhibitory effects of secondary metabolites on microbial CH4 production in heartwood reduce the CH4 emissions from the stems of living trees in upland forests.

Purpose Multiple anthropogenic disturbances, such as climate warming and nitrogen deposition are affecting terrestrial ecosystems. Different disturbances may have some consistent effects on the soil microbial community, which remains largely unexplored. Methods We mimicked 16 anthropogenic disturbances in a steppe ecosystem, and measured the absolute abundance and taxonomic composition of soil bacterial communities with qPCR and amplicon sequencing, respectively. Results We found that while the absolute abundance of each of the four dominant bacterial phyla did not show a consistent response to these disturbances, that of the five subdominant phyla showed a consistent increase. Meanwhile, these disturbances consistently stimulated the relative abundances of metabolic functions for high-growth-yield, including the transport/metabolism of amino acids and carbohydrates. Stochastic processes (e.g., random birth) played more critical roles in structuring the subdominant than dominant phyla, and the disturbances promoted the stochastic processes. Conclusions Overall, the high-yield traits and stochasticity of subdominant phyla led to their positive responses to disturbances. Furthermore, our findings indicate that the intensifying human activities are likely to cause a high-yield-strategies-toward shift in soil microbial composition in the Eurasian steppe ecosystem.

Random migration often plays important roles in soil microbial community assembly. However, it remains unexplored that whether its role is affected by anthropogenic disturbances, and whether the effects of different disturbances are consistent. Here, we report a novel and general pattern that different disturbances consistently restrain the role of migration in soil bacterial community assembly. We mimicked 16 types of anthropogenic disturbances relevant to a Eurasian steppe ecosystem, including removing different number of plant functional groups, mowing, adding nitrogen, adding phosphorus, watering, warming, and some of their combinations. The estimated migration rates in soil bacterial community assembly with Stephen Hubbell’s neutral model decreased by 0.19–6.29% under these disturbances. The relative change in migration rate was correlated with the deterministic change in community composition and the relative change in soil pH. Our results suggested that the intensifying anthropogenic disturbances may restrain the random dispersal, colonization and distribution of soil microorganisms.

Anthropogenic disturbances may decrease as we take measures to control them. However, the patterns and mechanisms of post-disturbance ecosystem succession have rarely been studied. Here we reported that disturbance level determined the importance of stochastic relative to deterministic changes in ecosystem components (plant community composition, soil microbial community composition, and soil physicochemical indices), and thus predefined the pattern of post-disturbance ecosystem succession. We proposed a theoretical framework with five disturbance levels corresponding to distinct succession patterns. We conducted a nitrogen addition experiment in a temperate steppe, monitored these ecosystem components during “disturbance” treatment (2010–2014) and post-treatment “succession” (2014–2018). The disturbance level experienced by each component in each treatment was inferred by fitting the observed succession patterns into the theoretical framework. The mean disturbance level of these components was found to increase quadratically with nitrogen addition rate. This was because increasing nitrogen addition reduced the importance of stochastic relative to deterministic changes in these components, and these changes had a quadratic relationship with disturbance level. Overall, our results suggested that by monitoring the importance of stochastic relative to deterministic changes in an ecosystem, we can estimate disturbance levels and predict succession patterns, as well as propose disturbance-level-dependent strategies for post-disturbance restoration.

Understanding species responsiveness to anthropogenic environmental changes benefits the guide to manage biodiversity. Microbes are traditionally thought to be more sensitive to environmental changes than plants. However, this hypothesis is supported by little empirical evidence. We compared plant and microbial responses to 13 types of simulated environmental changes (mowing (M), adding nitrogen (N), adding phosphorus (P), watering (W), warming (T) and combinations of these) in a steppe ecosystem. Contrary to our hypothesis, the microbial responses were generally smaller than the plant responses to different types of environmental changes, both at the community-abundance level and species/operational taxonomic unit (OTU)/gene level. This might be ascribed to the soil buffering capacity to environmental changes, and the rapid evolutionary adaptation for microbial communities. Furthermore, the responses at the community-abundance level were larger than at the species/OTU/gene level to 13 types of environmental changes, both in plant and microbial communities. Given that the community abundance representing the total number of all individuals of the organism within the community, the responses to environmental changes at the community-abundance level is likely to be larger than at the species/OTU/gene level. Plant biomass was more responsive to N addition, particularly in such N- limiting grassland ecosystem. Our findings highlight that plant communities are more responsive to environmental changes than microbial communities, contrary to the traditional viewpoint. Therefore, plant communities could be used as ecological indicators of anthropogenic environmental changes in grasslands. Keywords: Plant community, Microbial community, Anthropogenic environmental changes, Grassland, Abundance, Species/OTU/Gene number

Different environmental changes may have some consistent effects on soil microbial community, which remains largely unexplored. Here, we report a novel and general pattern that different environmental changes consistently selected for the sub-dominant soil bacterial phyla. We mimicked 16 types of environmental changes relevant to the Eurasian steppe ecosystem, including removing different number of plant functional groups, mowing, nitrogen adding, phosphorus adding, watering, warming, and some of their combinations. While the absolute abundance of each of the four dominant bacteria phyla (Acidobacteria, Actinobacteria, Chloroflexi, and Proteobacteria) did not show a consistent response to these treatments, that of the five sub-dominant phyla (Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospirae, and Planctomycetes) showed a consistent increase. The dominant phyla had high abundances of genes responsible for energy production/conversion and transcription, exhibiting oligotrophic traits; in contrast, the sub-dominant phyla had high abundance of 16S rDNA sequences, which could be due to greater rRNA copy number or smaller genomes, showing large growth/propagation potential and copiotrophic trait. Stochastic processes (e.g., random birth, death, colonization) played more important roles in structuring the sub-dominant than dominant phyla, and the treatments promoted the stochastic processes. The copiotrophy and stochasticity of sub-dominant phyla led to their positive responses to the treatments.

Our results demonstrated increased ecosystem nitrogen and water content as the primary drivers of the core and accessory components of soil microbial community functional diversity, respectively. Our findings suggested that more attention should be paid to certain components of community functional diversity under specific global change conditions. Our findings also indicated that microbial communities have adapted to nitrogen addition by strengthening the function of ammonia oxidization to deplete the excess nitrogen, thus maintaining ecosystem homeostasis. Because community gene richness is primarily determined by the presence/absence of accessory community genes, our findings further implied that strategies such as maintaining the amount of soil organic matter could be adopted to effectively improve the functional gene diversity of soil microbial communities subject to global change factors., It is a central ecological goal to explore the effects of global change factors on soil microbial communities. The vast functional gene repertoire of soil microbial communities is composed of both core and accessory genes, which may be governed by distinct drivers. This intuitive hypothesis, however, remains largely unexplored. We conducted a 5-year nitrogen and water addition experiment in the Eurasian steppe and quantified microbial gene diversity via shotgun metagenomics. Nitrogen addition led to an 11-fold increase in the abundance (based on quantitative PCR [qPCR]) of ammonia-oxidizing bacteria, which have mainly core community genes and few accessory community genes. Thus, nitrogen addition substantially increased the relative abundance of many core genes at the whole-community level. Water addition stimulated both plant diversity and microbial respiration; however, increased carbon/energy resources from plants did not counteract increased respiration, so soil carbon/energy resources became more limited. Thus, water addition selected for microorganisms with genes responsible for degrading recalcitrant soil organic matter. Accordingly, many other microorganisms without these genes (but likely with other accessory community genes due to relatively stable average microbial genome size) were selected against, leading to the decrease in the diversity of accessory community genes. In summary, nitrogen addition primarily affected core community genes through nitrogen-cycling processes, and water addition primarily regulated accessory community genes through carbon-cycling processes. Although both gene components may significantly respond as the intensity of nitrogen/water addition increases, our results demonstrated how these common global change factors distinctly impact each component. IMPORTANCE Our results demonstrated increased ecosystem nitrogen and water content as the primary drivers of the core and accessory components of soil microbial community functional diversity, respectively. Our findings suggested that more attention should be paid to certain components of community functional diversity under specific global change conditions. Our findings also indicated that microbial communities have adapted to nitrogen addition by strengthening the function of ammonia oxidization to deplete the excess nitrogen, thus maintaining ecosystem homeostasis. Because community gene richness is primarily determined by the presence/absence of accessory community genes, our findings further implied that strategies such as maintaining the amount of soil organic matter could be adopted to effectively improve the functional gene diversity of soil microbial communities subject to global change factors.

It is a central goal of current community ecology to explore the pattern and mechanism of community response to anthropogenic disturbances. Most researches focus on the response of community composition, which is based on the presence/absence or relative abundances of different species. However, the response of species-identity-independent community structure, such as the rank-abundance distribution, remains relatively understudied. We conducted a ten-year nitrogen addition experiment in a temperate steppe, with nine nitrogen rates under fencing (un-mowed) or mowing conditions. Mowing and nitrogen addition significantly altered both the composition and structure of plant communities. While the relative importance of stochastic change in community composition under mowing was not significantly different from that under fencing, the relative importance of stochastic change in community structure under mowing was significantly larger than that under fencing. Overall, our results demonstrated that mowing led to different drivers for the community composition and structure, meaning that mowing promoted the stochastic allocation of material and energy in primary producers in the grassland ecosystem.

Increasing atmospheric nitrogen (N) deposition causes profound changes in the plant community, significantly threatening the terrestrial ecosystem function and stability worldwide. Random migration is a primary determinant of plant community assembly in the neutral model. However, whether its role is affected by N deposition is obscure. Therefore, the effects of eight N application rates (0, 1, 2, 3, 5, 10, 15, and 20 g N m−2 yr−1) on the estimated migration rate of plant community were examined in a long-term field study in a semiarid steppe. Our results indicated that N addition significantly impacted the estimated migration rate (F = 4.89, P

Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity.

Many anthropogenic environmental changes are leading to a rapid decline in soil microbial functional diversity. However, ecological mechanisms that can serve to counteract/resist the diversity loss remain largely underexplored. In particular, although intermediate disturbance and increased amount of effective resources can promote the diversity of higher organisms, the potential role of these factors, and their combination, in maintaining microbial functional diversity is poorly studied. We conducted a 5-year experiment in a Eurasian steppe, manipulating mowing, nitrogen addition, phosphorus addition and their combinations. Nitrogen addition decreased soil pH by ~0.6 and bacterial abundance by ~19.5%, causing a disturbance effect. Phosphorus addition significantly decreased the effective amount of soil carbon-, nitrogen-, phosphorus- and water-relevant resources. Across all nitrogen-addition treatments subject to intermediate disturbance, there was a significant positive correlation between soil effective resource amount and microbial gene richness (r0.6, p0.01), which was elevated, in part, due to the increased fungal abundance. In contrast, significant correlations between gene richness and resource amount were not found under low-disturbance conditions. Overall, gene richness was greatest under conditions of both intermediate disturbance and ample effective resources, suggesting that the two factors could be manipulated in combination for the maintenance of microbial functional diversity.

A central goal in soil microbial ecology research is to identify the biodiversity patterns and reveal the underlying mechanisms. Long-term soil acidification is known to reduce soil bacterial diversity, but the mechanisms responsible for this pattern have not been well explored. Soil acidification may reduce bacterial richness through ecological filtering (EF). In contrast, two types of processes may promote the maintenance of bacterial richness: species may adapt to the acidic pressure through evolution, and endemic species already adapted to the acidic pressure can colonize the acidified soils through dispersal. To identify the relative contribution of EF and evolution/dispersal (ED), we collected soils with a pH range of 4–7 from different ecosystems, conducted an acidification experiment with a similar pH range in a neutral soil, and proposed a conceptual framework that could distinguish the three potential types of mechanism (neither EF nor ED operate; EF operates alone; ED counteracts some effect of EF). We found that the entire bacterial domain was driven by the third type of mechanism, with ED counteracting about 42.4% (95% confidence interval: 32.7–50.4%) effect of EF. Meanwhile, different bacterial phyla/classes were governed by different types of mechanisms, and the dominant was the third type. Our results highlight the importance of both ecological and evolutionary mechanisms for regulating soil bacterial communities under environmental changes.

In many grassland ecosystems, mowing, nitrogen (N) addition, and watering are carried out to improve plant productivity for the development of livestock husbandry. However, as a result of human activities, N deposition rate is predicted to increase and precipitation is expected to change. These environmental changes affect biodiversity and ecosystem functioning, and most of the previous studies have primarily focused on their effects on macro-organisms, neglecting the responses of soil microbial communities. In this study, we examined the changes in three community attributes (abundance, richness, and composition) of the entire bacterial kingdom and 16 dominant bacterial phyla/classes in response to mowing, N addition, watering, and their combinations, by conducting a 5-year experiment in a steppe ecosystem in Inner Mongolia, China. Overall, various bacterial groups responded differentially to these experimental treatments, with Acidobacteria, Proteobacteria, Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria being the most sensitive. Furthermore, the treatments produced different effects, with N addition and watering having much greater effects than mowing. Addition of N primarily affected these bacterial groups by reducing soil pH, while watering affected the bacterial groups by elevating both soil water content and soil pH. As N addition and watering had contrasting effects on soil pH, they also produced counteractive effects on many bacterial groups. The counteractive effects of N addition and watering suggest that the combination of these two treatments or the concurrence of N deposition and increased precipitation may be helpful for the maintenance of soil bacterial diversity and their ecosystem functions.

Identifying soil microbial feedbacks to increasing temperatures and moisture alterations is critical for predicting how terrestrial ecosystems will respond to climate change. We performed a 5-year field experiment manipulating warming, watering and their combination in a semiarid temperate steppe in northern China. Warming stimulated the abundance of genes responsible for degrading recalcitrant soil organic matter (SOM) and reduced SOM content by 13%. Watering, and warming plus watering also increased the abundance of recalcitrant SOM catabolism pathways, but concurrently promoted plant growth and increased labile SOM content, which somewhat offset SOM loss. The treatments also increased microbial biomass, community complexity and metabolic potential for nitrogen and sulfur assimilation. Both microbial and plant community composition shifted with the treatment conditions, and the sample-to-sample compositional variations of the two communities (pairwise β-diversity distances) were significantly correlated. In particular, microbial community composition was substantially correlated with the dominant plant species (~0.54 Spearman correlation coefficient), much more than with measured soil indices, affirming a tight coupling between both biological communities. Collectively, our study revealed the direction and underlying mechanisms of microbial feedbacks to warming and suggested that semiarid regions of northern steppes could act as a net carbon source under increased temperatures, unless precipitation increases concurrently.

Nitrogen deposition is changing biodiversity on Earth. We need to understand the underlying mechanisms to conserve biodiversity better. Both selection and chance are potential mechanisms, and they may operate concurrently. Then, what are the respective effects of selection and chance, what is their relative importance and how do they change with increasing nitrogen deposition rate? Here, we performed a 6-year nitrogen addition experiment (0-28 g N/m(2) /year) in a typical steppe ecosystem of Inner Mongolia to investigate the community structure of plants, bacteria and ammonia-oxidizing Archaea (AOA). We developed an experimentally based calculation method to first separate the structural variations between plots into the effects of selection (S) and chance (C), and then calculate their relative importance. Our results showed that as nitrogen addition rate increased, S for both plants and bacteria increased, but C for plants first increased and then decreased, and C for bacteria also increased; meanwhile, both S and C for AOA changed nonlinearly. As nitrogen addition rate increased, the importance of chance decreased on the whole for all these communities, but it decreased nonlinearly for plants and bacteria, with a local increase at certain intermediate rates. At all treatments, the importance of chance was 0.5 for AOA. These results demonstrated that nitrogen deposition changed biodiversity by mediating the effects and importance of chance, implicating different strategies should be adopted in conserving biodiversity according to nitrogen deposition rate and community properties.

Many investigations across natural and artificial plant diversity gradients have reported that both soil physicochemical factors and plant community composition affect soil microbial communities. To test the effect of plant diversity loss on soil bacterial communities, we conducted a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia (China). We found that the number and composition type of plant functional groups had no effect on bacterial diversity and community composition, or on the relative abundance of major taxa. In contrast, bacterial community patterns were significantly structured by soil water content differences among plots. Our results support researches that suggest that water availability is the key factor structuring soil bacterial communities in this semi-arid ecosystem.

In many grassland ecosystems, nitrogen (N) and phosphorus (P) are added to improve plant productivity, and the aboveground plant biomass is mowed and stored as hay for the bullamacow. Nutrient addition and mowing affect the biodiversity and ecosystem functioning, and most of the previous studies have primarily focused on their effects on macro-organisms, neglecting the responses of soil microbial communities. In this study, we examined the changes in three community attributes (abundance, richness, and composition) of the entire bacterial kingdom and 16 dominant bacterial phyla/classes in response to mowing, N addition, P addition, and their combinations, by conducting a 5-year experiment in a steppe ecosystem in Inner Mongolia, China. Overall, N addition had a greater effect than mowing and P addition on most of these bacterial groups, as indicated by changes in the abundance, richness and composition in response to these treatments. N addition affected these soil bacterial groups primarily through reducing soil pH and increasing available N content. Meanwhile, the 16 bacterial phyla/classes responded differentially to these experimental treatments, with Acidobacteria, Acidimicrobidae, Deltaproteobacteria, and Gammaproteobacteria being the most sensitive. The changes in the abundance, richness, and composition of various bacterial groups could imply some potential shift in their ecosystem functions. Furthermore, the important role of decreased soil pH caused by N addition in affecting soil bacterial communities suggests the importance of restoring acidified soil to maintain soil bacterial diversity.

Climate warming and shifting precipitation regimes are affecting biodiversity and ecosystem functioning. Most studies have focused on the influence of warming and altered precipitation on macro-organisms, whereas the responses of soil microbial communities have been neglected. We studied the changes in the abundance, richness, and composition of the entire bacterial kingdom and 16 dominant bacterial phyla/classes in response to increased precipitation, warming, and their combination, by conducting a 5-year experiment in a steppe ecosystem in Inner Mongolia, China. Watering had a greater effect than warming on almost all the bacterial groups as indicated by changes in all the three attributes (abundance, richness, and composition). The 16 phyla/classes responded differentially to the experimental treatments, with Acidobacteria and Gamma-proteobacteria being the most sensitive. Stepwise regression analyses further revealed that climate changes altered the abundance and richness of bacterial groups primarily through direct routes (e.g., increasing soil water content), and changed the community composition through both direct and indirect routes (e.g., reducing soil total nitrogen content and increasing soil pH). The diverse responses of various bacterial groups could imply some potential shift in their ecosystem functions under climate changes; meanwhile, the indirect routes that are important in altering bacterial composition suggest that specific strategies (e.g., adding NH4NO3 to maintain soil nitrogen content and pH) could be adopted to maintain soil microbial composition under climate changes.