● Bacterial networks became less connected with soil development along primary succession.

In microbial ecology, there is limited understanding of the mechanisms governing patterns in community structure across space and time. Here, we studied the changes of bacterial co-occurrence network structure over four primary successional soils after glacier retreat, including a sand dune system and three glacier foreland series, varying in timescale from centuries to millennia. We found that in all series, network structure was most complex in the earliest stages of succession, and became simpler over time. Richness and abundance of keystone species and network stability also declined over time. It appears that with less productive, nutrient poor and physiologically extreme conditions of early succession, closer interactions among bacterial species are ecologically selected for. These may take the form of consortia (with positive interactions) or stronger niche exclusion (with negative interactions). Additionally, we quantified the relative roles of different structuring processes on bacterial community using a bin-based null model analysis (iCAMP). With each successional series, community composition was initially governed by stochasticity, but as succession proceeded there was a progressive increase in deterministic selection over time, correlated with decreasing pH. Overall, our results show a consistency among the four series in long-term processes of community succession, with more integrated networks and greater stochasticity in early stages.

● Herbicide-based weeds control impacts wheat crops as well.

To address environmental concerns and manage resistant weeds, there is a growing demand for eco-friendly alternatives. In this study, we propose the integration of synthetic communities (SynComs) to reduce herbicide consumption. Four SynComs, consisting of bacteria isolated from weed or wheat rhizospheres, were first evaluated under greenhouse conditions. All SynComs enhanced wheat growth, which was manifested by increased Soil Plant Analysis Development (SPAD) values and fresh biomass. At the same time, SynCom C4 effectively reduced SPAD values and fresh biomass of the infesting weed, Phalaris minor, when combined with low-dose Axial herbicide. A field trial was then conducted using the C4 SynCom and various doses of Axial (100%, 75%, 50%, and 25%). Remarkably, the combination of C4 with 50% and 75% Axial significantly improved wheat growth by mitigating the side effects of herbicide on wheat. Weed infestation reduced grain yield by 16% and 25% at the dose of 50% and 75% Axial, respectively. The combination of Axial with C4 rescued up to 22% of grain yield loss under infested weed compared with Axial alone. Our findings suggested that the combination of herbicides with SynComs exhibited synergistic effects for controlling Phalaris minor and promoting wheat growth, so that such combination provides a sustainable and eco-friendly weed control strategy.

● CH₄ emission rates followed an increased pattern during the growing season at Tibetan Plateau.

Microorganisms play pivotal roles in soil methane (CH₄) emissions and their functional genes are origins of a key mechanism for soil CH₄-cycling. However, understanding of the roles of specific genes (e.g., unique or shared genes carried by species) underlying CH₄-cycling remains elusive. Here, we measured CH₄ emission rates and investigated variations in microbial community and the abundance of genes carried by species during the growing season in alpine meadow on the Tibetan Plateau. We discovered that CH₄ emission rates increased from 394.4, 745.9, and 1092.7 µg CH₄ m⁻² h⁻¹, in April, June, and August, respectively, and had a positive correlation with unique genes carried by abundant species during the growing season. Moreover, we found that unique genes carried by abundant species involved in methanogenesis processes have a higher abundance than methanotrophic processes. Further analysis indicated that climate factors (i.e., mean monthly temperature (MMT) and mean monthly precipitation (MMP)) influenced microbial community and their functional genes, and therefore affected the CH₄ emission rates. Overall, the present study provides a novel insight into the variation of soil CH₄ emissions from a functional gene perspective, highlighting the important roles of unique genes carried by abundant species in CH₄ emissions in the Tibetan Plateau under seasonal variation.

● N fertilizer altered bacterial community compositions by changing soil nutrients.

Nitrogen (N) fertilization drives the structure and function of soil microbial communities, which are crucial for regulating soil biogeochemical cycling and maintaining ecosystem stability. Despite the N fertilizer effects on soil microbial composition and diversity have been widely investigated, it is generally overlooked that ecosystem processes are carried out via complex associations among microbiome members. Here, we examined the effects of five N fertilization levels (0, 135, 180, 225, and 360 kg N ha⁻¹) on microbial co-occurrence networks and key functional taxa such as ammonia-oxidizers in paddy soils. The results showed that N addition altered microbial community composition, which were positively related to soil total N and available phosphorus (P) contents. The abundance of ammonia-oxidizing archaea (AOA) significantly decreased after N addition, whereas ammonia-oxidizing bacteria (AOB) increased in N360 treatment. Compared with low-N group (N0 and N135), the high-N group (N225 and N360) shaped more complex microbial webs and thus improved the stability of the microbial community. Partial least squares path modeling further revealed that N fertilizer had a higher effect on microbial network complexity in the high-N group (0.83) than the low-N group (0.49). Although there were more positive links across all microbial networks, the proportion of negative links significantly increased in the high-N network, suggesting that excess N addition aggravated the competition among microbial species. Disentangling these interactions between microbial communities and N fertilization advances our understanding of biogeochemical processes in paddy soils and their effects on nutrient supply to rice production. Our findings highlighted that highly N-enriched paddy soils have more stable microbial networks and can better sustain soil ecological functions to cope with the ongoing environmental changes.

● Microbial attributes were compared between soil fauna gut and plant rhizosphere.

Diverse microbes inhabit animals and plants, helping their hosts perform multiple functions in agricultural ecosystems. However, the responses of soil fauna gut and plant rhizosphere microbiomes to livestock manure applications are still not well understood. Here we fed Protaetia brevitarsis larvae (PBL) with chicken manure and collected their frass. The frass and manure were applied as fertilizers to lettuce pots. We then compared the changes of microbial diversity, community assembly, and potential functions between the gut group (i.e., all PBL gut and frass samples) and the rhizosphere group (i.e., all rhizosphere soil samples). We revealed that manure applications (i.e., feeding or fertilization) decreased bacterial diversity in the gut group but increased that in the rhizosphere group. Particularly, the proportions of Bacilli in the gut group and Gammaproteobacteria in the rhizosphere group were increased (up to a maximum of 33.8% and 20.4%, respectively) after manure applications. Stochastic and deterministic processes dominated community assembly in the gut and rhizosphere microbiomes, respectively. Manure applications increased the microbial co-occurrence network complexity of both the gut and rhizosphere groups. Moreover, the proportions of functional taxa associated with human/animal pathogens in the gut group and carbon/nitrogen cycling in the rhizosphere group were enhanced (up to 2.6-fold and 24.6-fold, respectively). Our findings illustrate the different responses of microbial diversity, community assembly, and potential functions in soil fauna gut and plant rhizosphere to manure applications. The results could enhance our knowledge on the reasonable utilization of animal and plant microbiomes in agricultural management.

• Volcanic inputs and grazing impact the distribution of microbes in Serengeti soil.

As one of the last remaining naturally grazed ecosystems on Earth, the Serengeti National Park is an ideal location to study the influence of migratory mammals on the structure of microbial communities and the factors that generate biogeography of soil microbes. Furthermore, volcanic inputs generate environmental gradients that may also structure microbial communities. We studied 16S rRNA amplicons in a 13-year herbivore removal experiment to examine the influence of grazing and environmental gradients on the natural distribution of soil microbes. Removal of mammalian herbivores shifted microbial community structure, with 31 taxa that were significant indicator taxa of the ungrazed treatment and three taxa that were indicators of the grazed treatment. The abundance of many taxa were correlated with soil texture, phosphorus, iron, calcium and rainfall, and the evenness of taxa within samples was also correlated with these variables. Bayesian general linear mixed effects models with single predictors of multiple, highly correlated variables of beta diversity were consistent with a significant, but weak (2%), effect of grazing, and stronger effects of phosphorus (14%). Beta diversity of microbial communities was greater in grazed than in ungrazed plots; suggesting that the impacts of grazing on community assembly of microbes results from deterministic environmental filtering caused by the influence of herbivores on plant communities and soil properties rather than stochastic dispersal via herds of large mammals. These herbivore effects are superimposed on deterministic environmental filtering by natural soil and precipitation gradients across the Serengeti.