Unravelling the effects of tropical land use conversion on the soil microbiome

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

BACKGROUND

Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.

RESULTS

After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).

CONCLUSION

Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.

Enhancing tomato disease resistance through endogenous antifungal proteins and introduced nematode-targeting dsRNA of biocontrol agent Bacillus velezensis HS-3

BACKGROUND

As a type of biological control agent (BCA), Bacillus velezensis possesses the efficacy of inhibiting pathogenic microorganisms, promoting plant growth, and overcoming continuous cropping obstacles (CCOs). However, there is limited reporting on the optimization of the cultivation conditions for such biocontrol agents and their role as double-stranded RNA (dsRNA) delivery vectors.

RESULTS

In this study, a Bacillus velezensis strain HS-3 was isolated from the root zone of tomato plants with in vitro anti-Botrytis cinerea activity. The investigation into active compounds revealed that HS-3 predominantly employs proteins with molecular weights greater than 3 kDa for its antifungal activity. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified various proteases and chitosanase, further suggesting that HS-3 most likely employs these enzymes to degrade fungal cell walls for its antifungal effect. To optimize the production of extracellular proteins, fermentation parameters for HS-3 were systematically optimized, leading to an optimized medium (OP-M). HS-3 cultured in OP-M demonstrated enhanced capacity to assist tomato plants in withstanding CCOs. However, the presence of excessive nematodes in diseased soil resulted in the disease severity index (DSI) remaining high. An RNA interference mechanism was further introduced to HS-3, targeting the nematode tyrosine phosphatase (TP) gene. Ultimately, HS-3 expressing dsRNA of TP in OP-M effectively assisted tomatoes in mitigating CCOs, reducing DSI to 2.2% and 17.8% of the control after 45 and 90 days of growth, respectively.

CONCLUSION

The advantages of Bacillus velezensis in crop disease management and the mitigation of CCOs become even more pronounced when utilizing both optimized levels of endogenous enzymes and introduced nematode-targeting dsRNA. © 2024 Society of Chemical Industry.

Land use change alters carbon and nitrogen dynamics mediated by fungal functional guilds within soil aggregates

Land use change is one of the greatest threats to soil biodiversity and ecological functions; however, how such a transition affects soil carbon (C) and nitrogen (N) dynamics driven by fungal communities at the aggregate level remains unclear. Here, we explored the variation in soil C and N pools, specific enzyme activities and fungal communities and functional guilds within three aggregate sizes (megaaggregates, > 2 mm; macroaggregates, 0.25-2 mm; microaggregates, < 0.25 mm) in a natural forest, 12- and 24-year-old rubber monocultures and corresponding agroforestry systems in tropical China. Tropical forest conversion to rubber monocultures generally reduced C and N pools in all aggregates, while agroforestry systems decreased microbial biomass C and N. Carbon- and N-degrading enzyme activities responded differently to forest conversion and were enhanced in agroforestry systems. The levels of C and N pools and their related enzyme activities increased as the aggregate size decreased. Moreover, fungal compositional shifts in dominance from copiotrophic Ascomycota and Basidiomycota (r-strategists) into oligotrophic Zygomycota (K-strategists) were noted following forest conversion, resulting in more pathogenic fungi at the expense of saprotrophic and arbuscular mycorrhizal fungi. Pathogenic fungi were greatly inhibited due to abundant Mortierella after the establishment of 12-year-old agroforestry systems. The diversity of saprotrophic fungi was the highest in microaggregates. Regardless of land use type, aggregate-associated C and N pools, especially DOC, MBC, NO3--N and DON in microaggregates, were interactively mediated by functional guilds of fungi, which was primarily driven by soil pH. These results highlight the importance of fungal functional guilds in determining C and N dynamics at the aggregate level and provide insights into the sustainable management of cash tree plantations.

Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds

Shrimp farming is blooming worldwide, posing a severe threat to mangroves and its multiple goods and ecosystem services. Several studies reported the impacts of aquaculture on mangrove biotic communities, including microbiomes. However, little is known about how mangrove soil microbiomes would change in response to mangrove forest recolonization. Using genome-resolved metagenomics, we compared the soil microbiome of mangrove forests (both with and without the direct influence of shrimp farming effluents) with active shrimp farms and mangroves under a recolonization process. We found that the structure and composition of active shrimp farms microbial communities differ from the control mangrove forests, mangroves under the impact of the shrimp farming effluents, and mangroves under recolonization. Shrimp farming ponds microbiomes have lower microbial diversity and are dominated by halophilic microorganisms, presenting high abundance of multiple antibiotic resistance genes. On the other hand, control mangrove forests, impacted mangroves (exposed to the shrimp farming effluents), and recolonization ponds were more diverse, with a higher abundance of genes related to carbon mobilization. Our data also indicated that the microbiome is recovering in the mangrove recolonization ponds, performing vital metabolic functions and functionally resembling microbiomes found in those soils of neighboring control mangrove forests. Despite highlighting the damage caused by the habitat changes in mangrove soil microbiome community and functioning, our study sheds light on these systems incredible recovery capacity. Our study shows the importance of natural mangrove forest recovery, enhancing ecosystem services by the soil microbial communities even in a very early development stage of mangrove forest, thus encouraging mangrove conservation and restoration efforts worldwide.

Adaptive changes of coral Galaxea fascicularis holobiont in response to nearshore stress

Global change and local stressors are simultaneously affecting the nearshore corals, and microbiome flexibility may assist corals in thriving under such multiple stressors. Here, we investigated the effects of various environmental variables on Galaxea fascicularis holobiont from nearshore and offshore reefs. These nearshore reefs were more turbid, eutrophic, and warm than offshore reefs. However, coral physiological parameters did not differ significantly. Corals under stressful nearshore environments had low symbiont diversity and selected more tolerant Symbiodiniaceae. The bacterial diversity of offshore corals was significantly higher, and their community composition varied obviously. Diffusion limitations and environmental heterogeneity were essential in structuring microbial communities. Functional annotation analysis demonstrated significant differences between nearshore and offshore corals in bacterial functional groups. Environmental stress significantly reduced the complexity and connectivity of bacterial networks, and the abundances of keystone taxa altered considerably. These results indicated that corals could thrive nearshore through holobiont plasticity to cope with multiple environmental stresses.

Plant Growth Promotion and Biocontrol by Endophytic and Rhizospheric Microorganisms From the Tropics: A Review and Perspectives

Currently, the tropics harbor a wide variety of crops to feed the global population. Rapid population expansion and the consequent major demand for food and agriculture-based products generate initiatives for tropical forest deforestation, which contributes to land degradation and the loss of macro and micronative biodiversity of ecosystems. Likewise, the entire dependence on fertilizers and pesticides also contributes to negative impacts on environmental and human health. To guarantee current and future food safety, as well as natural resource preservation, systems for sustainable crops in the tropics have attracted substantial attention worldwide. Therefore, the use of beneficial plant-associated microorganisms is a promising sustainable way to solve issues concerning modern agriculture and the environment. Efficient strains of bacteria and fungi are a rich source of natural products that might improve crop yield in numerous biological ways, such as nitrogen fixation, hormone production, mobilization of insoluble nutrients, and mechanisms related to plant biotic and abiotic stress alleviation. Additionally, these microorganisms also exhibit great potential for the biocontrol of phytopathogens and pest insects. This review addresses research regarding endophytic and rhizospheric microorganisms associated with tropical plants as a sustainable alternative to control diseases and enhance food production to minimize ecological damage in tropical ecosystems.

Assessing the contribution of mobility in the European Union to rubber expansion

Nearly three-quarters of global natural rubber production is used to produce tyres, supporting mobility around the globe. The projected increase in mobility could contribute to further expansion of rubber plantations and impact tropical ecosystems. We quantified the use of natural rubber in tyres in the European Union (EU), the corresponding land footprint, and explored drivers of tyre use using country-specific transport statistics and trade registers of rubber goods. Five percent of the world's natural rubber is consumed in tyres used in the EU, using up to a quarter of the area under rubber plantations in some producing countries. Car use is responsible for 58% of this consumption, due to car-dependent lifestyles that are associated with economic prosperity and spatial planning paradigms. While the EU's transport policy focuses on reducing dependence on fossil-fuels, cross-cutting policies are needed to address car-dependency and reduce the EU's land footprint in tropical landscapes without compromising progress towards decarbonisation.

Response of Functional Diversity of Soil Microbial Community to Forest Cutting and Regeneration Methodology in a Chinese Fir Plantation

With the expansion of pure forest planting area and the increase in the number of rotations used, soil activity and plant productivity have significantly reduced. The functional diversity of soil microorganisms plays a vital role in forest health and the long-term maintenance of productivity. Though the optimization of forest cutting and regeneration methodologies is necessary to improve the functional diversity of soil microorganisms, the effects of harvest residual treatment on the functional diversity of soil microorganisms remain unclear. During the period 2018–2020, we designed four harvest residual treatments—reference (RF), residual burning (RB), crushing and mulching (MT), and no residuals (NR)—to determine soil physical and chemical properties. We also used microbial biomass (MB) to evaluate the diversity in carbon source metabolism of soil microorganisms through Biolog microplate technology, and discussed the response mechanism of microbial functional diversity to the different forest cutting and regeneration methodologies used in Chinese fir plantations. The results indicated that RB significantly increased the carbon metabolic capacity of the microbial community, the community richness, and its dominance compared to RF, MT, and NR; however, they also showed that it decreased the uniformity of the soil microbial community. NR showed a poor carbon utilization capacity for microorganisms compared to RF and MT, while MT significantly increased the utilization capacity of carbohydrate and amino acid carbon compared with RF. Soil nutrients were the main driving factors of soil microbial carbon metabolic activity, and the different responses of microbial functional diversity to various forest cutting and regeneration methodologies were mainly due to the variation in the nutrient inputs of harvest residues. This study provides a practical basis for enhancing the functional diversity of soil microorganisms in plantations through the management of harvest residues.

Microbial characteristics of the leachate contaminated soil of an informal landfill site

Because informal landfills are not constructed in a regulated manner, they will inevitably become a source of leachate pollution to the surrounding environment over time. Microbes are an important part of the soil system, playing a vital role in maintaining the normal functionality of soil. This study investigated the microbial composition and co-occurrence pattern in the leachate contaminated soil of an informal landfill site. The landfill leachate underwent horizontal and vertical migration through the contaminated soil, resulting in significant differences in the microbial compositions of horizontal surface soil (CS) and vertical subsurface soil (DS and ES) compared to uncontaminated soil (S). The microbial diversity of CS, DS, and ES was lower than that of S. Due to the migration of landfill leachate, the microbial composition of the surface soil was substantially changed. The dominant phyla in S included Proteobacteria (26.88%), Chloroflexi (23.68%), Actinobacteroita (17.36%), and Acidobacteroita (16.86%), but in contaminated soils, Firmicutes (35.27-86.68%) were the dominant bacteria. A network analysis indicated that Bacilli, Clostridia, and Thermacetogeniazai of the Firmicutes were the keystone taxa and played a vital role in maintaining the stability of the soil ecosystem. A functional annotation of prokaryotic taxa (FAPROTAX) analysis showed that the microbes involved in the C-, N-, and S-cycles in contaminated soil were significantly different to those in uncontaminated soil. The proportion of (aerobic)-chemoheterotrophy and cellulolysis functional communities in contaminated soils was significantly reduced, while there was an increase in functional communities, such as anammox and denitrification, which are not conducive to soil nitrogen fixation. This negatively affected the maintenance of normal soil ecological functions. This study identified the microbial characteristics in leachate contaminated soil and the results will be beneficial for the remediation of contaminated soil in informal landfill sites.

Forest conversion to plantations: A meta-analysis of consequences for soil and microbial properties and functions

Primary or secondary forests around the world are increasingly being converted into plantations. Soil microorganisms are critical for all biogeochemical processes in ecosystems, but the effects of forest conversion on microbial communities and their functioning remain unclear. Here, we conducted a meta-analysis to quantify the impacts that converting forests to plantations has on soil microbial communities and functioning as well as on the associated plant and soil properties. We collected 524 paired observations from 138 studies globally. We found that conversion leads to broad range of adverse impacts on soils and microorganisms, including on soil organic carbon (-24%), total nitrogen (-29%), bacterial and fungal biomass (-36% and -42%, respectively), microbial biomass carbon (MBC, -31%) and nitrogen (-33%), and fungi to bacteria ratio (F:B, -16%). In addition, we found impacts on the ratio of MBC to soil organic C (qMBC, -20%), microbial respiration (-18%), N mineralization (-18%), and enzyme activities including β-1,4-glucosidase (-54%), β-1,4-N-acetylglucosaminidase (-39%), and acid phosphatase (ACP; -34%). In contrast, conversion to plantations increases bacterial richness (+21%) and microbial metabolic quotient (qCO₂ , +21%). The effects of forest conversion were consistent across stand ages, stand types, and climate zone. Soil C and N contents as well as the C:N ratio were the main factors responsible for the changes of microbial C, F:B, and bacterial richness. The responses of qCO₂ , N mineralization, and ACP activity were mainly driven by the reductions in F:B, MBC, and soil C:N. Applying macro-ecology theory on ecosystem disturbance in soil microbial ecology, we show that microbial groups shifted from K to r strategists after conversion to plantations. Our meta-analysis underlines the adverse effects of natural forests conversion to plantations on soil microbial communities and functioning, and suggests that the preservation of soil functions should be a consideration in forest management practices.

Metagenomics Unveils Posidonia oceanica "Banquettes" as a Potential Source of Novel Bioactive Compounds and Carbohydrate Active Enzymes (CAZymes)

Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea. It produces large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." In recent years, interest in the potential uses of these P. oceanica banquettes has increased, and it was demonstrated that biomass extracts showed antioxidant, antifungal, and antiviral activities. The discovery of new compounds through the culture of microorganisms is limited, and to overcome this limitation, we performed a metagenomic study to investigate the microbial community associated with P. oceanica banquettes. Our results showed that the microbial community associated with P. oceanica banquettes was dominated by Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria. Pseudoalteromonas was the dominant genus, followed by Alteromonas, Labrenzia, and Aquimarina. The metagenome reads were binned and assembled into 23 nearly complete metagenome-assembled genomes (MAGs), which belonged to new families of Cyanobacteria, Myxococcota, and Granulosicoccaceae and also to the novel genus recently described as Gammaproteobacteria family UBA10353. A comparative analysis with 60 published metagenomes from different environments, including seawater, marine biofilms, soils, corals, sponges, and hydrothermal vents, indicated that banquettes have numbers of natural products and carbohydrate active enzymes (CAZymes) similar to those found for soils and were only surpassed by marine biofilms. New proteins assigned to cellulosome modules and lignocellulose-degrading enzymes were also found. These results unveiled the diverse microbial composition of P. oceanica banquettes and determined that banquettes are a potential source of bioactive compounds and novel enzymes. IMPORTANCE Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea that forms large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." These banquettes accumulate on the shore, where they can prevent erosion, although they also cause social concern due to their impact on beach use. Furthermore, Posidonia dry material has been considered a source of traditional remedies in several areas of the Mediterranean, and a few studies have been carried out to explore pharmacological activities of Posidonia extracts. The work presented here provides the first characterization of the microbiome associated with Posidonia banquettes. We carried out a metagenomic analysis together with an in-depth comparison of the banquette metagenome with 60 published metagenomes from different environments. This comparative analysis has unveiled the potential that Posidonia banquettes have for the synthesis of natural products, both in abundance (only surpassed by marine biofilms) and novelty. These products include mainly nonribosomal peptides and carbohydrate active enzymes. Thus, the interest of our work lies in the interest of Posidonia "waste" material as a source of new bioactive compounds and CAZymes.

Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories

Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO₃) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.

Conversion of rainforest into oil palm and rubber plantations affects the functional composition of litter and soil Collembola

Rainforest conversion and expansion of plantations in tropical regions are associated with changes in animal communities and biodiversity decline. In soil, Collembola are one of the most numerous invertebrate groups that affect the functioning of microbial communities and support arthropod predators. Despite that, information on the impact of changes in land use in the tropics on species and trait composition of Collembola communities is very limited. We investigated the response of Collembola to the conversion of rainforest into rubber agroforestry ("jungle rubber"), rubber, and oil palm plantations in Jambi Province (Sumatra, Indonesia), a region which experienced one of the strongest recent deforestation globally. Collembola were sampled in 2013 and 2016 from the litter and soil layer using heat extraction, and environmental factors were measured (litter C/N ratio, pH, water content, composition of microbial community and predator abundance). In the litter layer, density and species richness in plantation systems were 25%-38% and 30%-40% lower, respectively, than in rainforest. However, in the soil layer, density, species richness, and trait diversity of Collembola were only slightly affected by land-use change, contrasting the response of many other animal groups. Species and trait composition of Collembola communities in litter and soil differed between each of the land-use systems. Water content and pH were identified as main factors related to the differences in species and trait composition in both litter and soil, followed by the density of micro- and macropredators. Dominant species of Collembola in rainforest and jungle rubber were characterized by small body size, absence of furca, and absence of intense pigmentation, while in plantations, larger species with long furca and diffuse or patterned pigmentation were more abundant. Overall, land-use change negatively affected Collembola communities in the litter layer, but its impact was lower in the soil layer. Several pantropical genera of Collembola (i.e., Isotomiella, Pseudosinella, and Folsomides) dominated across land-use systems, reflecting their high environmental adaptability and/or efficient dispersal, calling for studies on their ecology and genetic diversity. The decline in species richness and density of litter-dwelling Collembola with the conversion of rainforest into plantation systems calls for management practices mitigating negative effects of the deterioration of the litter layer in rubber plantations, but even more in oil palm plantations.

Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas

Advancing extensive cattle production is a major threat to biodiversity conservation in Amazonia. The dominant vegetation cover has a drastic impact on soil microbial communities, affecting their composition, structure, and ecological services. Herein, we explored relationships between land-use, soil types, and forest floor compartments on the prokaryotic metacommunity structuring in Western Amazonia. Soil samples were taken in sites under high anthropogenic pressure and distributed along a ±800 km gradient. Additionally, the litter and a root layer, characteristic of the forest environment, were sampled. DNA was extracted, and metacommunity composition and structure were assessed through 16S rRNA gene sequencing. Prokaryotic metacommunities in the bulk soil were strongly affected by pH, base and aluminum saturation, Ca + Mg concentration, the sum of bases, and silt percentage, due to land-use management and natural differences among the soil types. Higher alpha, beta, and gamma diversities were observed in sites with higher soil pH and fertility, such as pasture soils or fertile soils of the state of Acre. When taking litter and root layer communities into account, the beta diversity was significantly higher in the forest floor than in pasture bulk soil for all study regions. Our results show that the forest floor's prokaryotic metacommunity performs a spatial turnover hitherto underestimated to the regional scale of diversity.

Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community

The continuous cropping of plants can result in the disruption of the soil microbial community and caused significant declines in yields. However, there are few reports on the effects of continuous cropping of sugarcane on the microbial community structure and functional pathway. In the current study, we analyzed the structural and functional changes of microbial community structure in the rhizospheric soil of sugarcane in different continuous cropping years using Illumina Miseq high-throughput sequencing and metagenomics analysis. We collected rhizosphere soils from fields of no continuous cropping history (NCC), 10 years of continuous cropping (CC10), and 30 years of continuous cropping (CC30) periods in the Fujian province. The results demonstrated that continuous sugarcane cropping resulted in significant changes in the physicochemical properties of soil and the composition of soil bacterial and fungal communities. With the continuous cropping, the crop yield dramatically declined from NCC to CC30. Besides, the redundancy analysis (RDA) of the dominant bacterial and fungal phyla and soil physicochemical properties revealed that the structures of the bacterial and fungal communities were mainly driven by pH and TS. Analysis of potential functional pathways during the continuous cropping suggests that different KEGG pathways were enriched in different continuous cropping periods. The significant reduction of bacteria associated with rhizospheric soil nitrogen and sulfur cycling functions and enrichment of pathogenic bacteria may be responsible for the reduction of effective nitrogen and total sulfur content in rhizospheric soil of continuous sugarcane as well as the reduction of sugarcane yield and sugar content. Additionally, genes related to nitrogen and sulfur cycling were identified in our study, and the decreased abundance of nitrogen translocation genes and AprAB and DsrAB in the dissimilatory sulfate reduction pathway could be the cause of declined biomass. The findings of this study may provide a theoretical basis for uncovering the mechanism of obstacles in continuous sugarcane cropping and provide better guidance for sustainable development of the sugarcane.

Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production

Interactions between microorganisms and host plants determine the growth and development as well as the health of the host plant. Various microbial groups inhabit the rhizosphere, each with its peculiar function. The survival of each microbial group depends to a large extent on its ability to colonize the plant root and outcompete the native organisms. The role of the rhizospheric microbiome in enhancing plant growth has not been fully maximized. An understanding of the complexities of microbial interactions and factors affecting their assembly in the community is necessary to benefit maximally from the cooperations of various microbial communities for sustainable crop production. In this review, we outline the various organisms associated with the plant rhizosphere with emphasis on their interactions and mechanisms used in plant growth promotion.

Characterization of the Aedes albopictus (Diptera: Culicidae) holobiome: bacterial composition across land use type and mosquito sex in Malaysia

Understanding the diversity and dynamics of the microbiota within the mosquito holobiome is of great importance to apprehend how the microbiota modulates various complex processes and interactions. This study examined the bacterial composition of Aedes albopictus across land use type and mosquito sex in the state of Selangor, Malaysia using 16S rRNA sequencing. The bacterial community structure in mosquitoes was found to be influenced by land use type and mosquito sex, with the environment and mosquito diet respectively identified to be the most likely sources of microbes. We found that approximately 70% of the microbiota samples were dominated by Wolbachia and removing Wolbachia from analyses revealed the relatively even composition of the remaining bacterial microbiota. Furthermore, microbial interaction network analysis highlighted the prevalence of co-exclusionary patterns in all networks regardless of land use and mosquito sex, with Wolbachia exhibiting co-exclusionary interactions with other residential bacteria such as Xanthomonas, Xenophilus and Zymobacter.

Soil bacterial community structures in relation to different oil palm management practices

We provide soil bacterial 16 S rRNA gene amplicon and geochemical data derived from an oil palm plantation management experiment. The experimental design covered two different intensities of fertilizer application and weeding practices. We sampled the topsoil of 80 plots in total and extracted DNA and RNA. 16 S rRNA gene-derived and transcript-derived amplicons were generated and sequenced to analyse community composition and beta-diversity. One year after establishing the experiment, statistically significant differences of bacterial diversity or community composition between different treatments at entire (DNA-derived) and active (RNA-derived) community level were not detected. The dominant taxa belonged to Acidobacteriota and Actinobacteriota and were more abundant in the active community compared to the entire community. Similarly, the abundant genera Candidatus Solibacter and Haliangium were more abundant at active community level. Furthermore, clustering corresponding to the different sampling site locations was detected. Beta-diversity did not change among the treatments at DNA and RNA level. This dataset is of interest for related studies on the effect of altered management practices on soilborne communities.

Asymmetric response of soil methane uptake rate to land degradation and restoration: Data synthesis

Land degradation and restoration profoundly affect soil CH₄ uptake capacity in terrestrial ecosystems. However, a comprehensive assessment of the response of soil CH₄ uptake to land degradation and restoration at global scale is not available. Here, we present a global meta-analysis with a database of 228 observations from 83 studies to investigate the effects of land degradation and restoration on the capacity of soil CH₄ uptake. We found that land degradation significantly decreased the capacity of soil CH₄ uptake, except the conversion of pasture to cropland where the soil CH₄ uptake rate showed no response. In contrast, all types of land restoration significantly increased the capacity of soil CH₄ uptake. Interestingly, the response of soil CH₄ uptake rate to land degradation and restoration was asymmetric: the increased soil CH₄ uptake rate in response to the land restoration was smaller compared to the decrease in CH₄ uptake rate induced by the land degradation. The effect of land degradation on soil CH₄ uptake rate was not dependent on the time since land use change, but the CH₄ sink strength increased with the time since land restoration. The response of soil CH₄ uptake rate to both land degradation and restoration was predominantly regulated by changes in the soil water-filled pore space, soil bulk density, and pH, whereas alterations in the substrate quantity and quality had negligible effect. Additionally, the effects of land degradation and restoration on soil CH₄ uptake were strongly related to the mean annual precipitation and soil texture. Overall, our results provide novel insights for understanding of how land degradation and restoration can affect the CH₄ sink strength of upland soils, and more importantly, our findings are beneficial to take measures to enhance the potential of soil CH₄ uptake in response to global land use change.

Biodegradation of natural rubber and deproteinized natural rubber by enrichment bacterial consortia

This study examined the biodegradation of natural rubber (NR) and deproteinized natural rubber (DPNR) by bacterial consortia enriched from a rubber-processing factory's waste in Vietnam. The results reveal the degradation in both NR and DPNR, and the DPNR was degraded easier than NR. The highest weight loss of 48.37% was obtained in the fourth enrichment consortium with DPNR, while 35.39% was obtained in the fifth enrichment consortium with NR after 14 days of incubation. Nitrogen content and fatty acid content determined by Kjeldahl method and fourier transform infrared spectroscopy (FTIR), respectively, were decreased significantly after being incubated with the consortia. Structure of degraded rubber film analyzed by nuclear magnetic resonance spectroscopy showed the presence of aldehyde group, a sign of rubber degradation. Bacterial cells tightly adhering and embedding into NR and DPNR films were observed by scanning electron microscopy. There were differences in the bacterial composition of the consortia with NR and DPNR, which were determined by metagenomic analysis using 16S rRNA gene sequencing. The phyla Bacteroidetes and Proteobacteria may play a role in the degradation of non-isoprene compounds such as protein or lipid, while the phylum Actinobacteria plays a crucial role in the degradation of rubber hydrocarbon in all consortia.