Functional Gene Structure Research Articles

Soil phosphorus cycling microbial functional genes of monoculture and mixed plantations of native tree species in subtropical China.

Transforming coniferous plantation into broadleaved or mixed broadleaved-coniferous plantations is the tendency of forest management strategies in subtropical China. However, the effects of this conversion on soil phosphorus (P) cycling microbial functional genes are still unknown. Soil samples were collected from 0-20, 20-40, and 40-60 cm (topsoil, middle layer, and subsoil, respectively) under coniferous Pinus massoniana (PM), broadleaved Erythrophleum fordii (EF), and their mixed (PM/EF) plantation in subtropical China. Used metagenomic sequencing to examine the alterations of relative abundances and molecular ecological network structure of soil P-cycling functional genes after the conversion of plantations. The composition of P-cycling genes in the topsoil of PM stand was significantly different from that of PM/EF and EF stands (p < 0.05), and total phosphorus (TP) was the main factor causing this difference. After transforming PM plantation into EF plantation, the relative abundances of P solubilization and mineralization genes significantly increased in the topsoil and middle layer with the decrease of soil TP content. The abundances of P-starvation response regulation genes also significantly increased in the subsoil (p < 0.05), which may have been influenced by soil organic carbon (SOC). The dominant genes in all soil layers under three plantations were phoR, glpP, gcd, ppk, and ppx. Transforming PM into EF plantation apparently increased gcd abundance in the topsoil (p < 0.05), with TP and NO3 --N being the main influencing factors. After transforming PM into PM/EF plantations, the molecular ecological network structure of P-cycling genes was more complex; moreover, the key genes in the network were modified with the transformation of PM plantation. Transforming PM into EF plantation mainly improved the phosphate solubilizing potential of microorganisms at topsoil, while transforming PM into PM/EF plantation may have enhanced structural stability of microbial P-cycling genes react to environmental changes.

Light grazing reduces the abundance of carbon cycling functional genes by decreasing oligotrophs microbes in desert steppe

Understanding the functional genes of microorganisms involved in carbon cycling processes can link microbial community structure to potential ecological functions. However, the effects of grazing on the relationship between carbon cycling functional genes and soil environment need to be further investigated as a global land use activity. A replicated sheep grazing platform was established in Northern China in 2004 with four different stocking rates: no grazing (0 sheep ha−1 month−1), light grazing (0.15 sheep ha−1 month−1), moderate grazing (0.30 sheep ha−1 month−1), and heavy grazing (0.45 sheep ha−1 month−1). To examine the effects of biotic and abiotic factors on microbial species and functional gene abundance, we collected soil samples after 17 years of grazing analyzed for the abundance of microbial communities, the abundance of carbon function genes, plant carbon input and soil environmental factors. We found that light grazing reduced carbon cycling functional genes compared to no grazing (fencing). With increasing grazing intensity, the absolute abundance of functional genes increased. Changes in microbial species abundance were mainly responsible for the changes in the structure of carbon cycling functional genes. Our results emphasize that elucidating how grazing affects the carbon cycling functional genes through the effects of plant carbon inputs and the environment, and the interactions between them, will provide important information for understanding carbon cycling processes in grassland ecosystems.

Soil ecosystem multifunctionality is strongly linked with crop yield after four decades chemical fertilization in black soil

Soil ecosystem multifunctionality (EMF), the ability of an ecosystem to perform multiple functions, remains uncertain in its contribution to crop production, especially in the context of long-term fertilization ecosystems. This study was carried out on a 40-year-old long-term fertilization experiment in black soil in China. Soil samples were collected from four treatments: control (CK); nitrogen (N) fertilizer; phosphorus (P) fertilizer; and a combination of nitrogen and phosphorus (NP) in both maize and wheat planting seasons. The results showed significant effects of N, P fertilizers and crop season on soil biotic and abiotic properties, especially on soil enzyme activities. Crop productivity and soil EMF showed a similar pattern across different treatments and both crop seasons, with significant higher values recorded in treatments with N addition (i.e. N and NP). Soil EMF was strongly associated with crop productivity in both maize and wheat seasons, while soil pH had a negative impact on crop yield. Random forest analysis revealed that microbial functional gene structure was significantly correlated with both soil ecosystem multifunctionality and crop yield. This suggested that fertilization leads to alterations in soil nutrients and the composition of functional microbial communities, subsequently impacting ecological functions and crop growth. These findings indicated that mineral fertilizers can enhance crop yield through soil EMF in the black soils, while exerted substantial impact on soil properties, raising concerns about the sustainability of soils under continuous chemical fertilization.

Nitrogen enrichment stimulates rhizosphere multi-element cycling genes via mediating plant biomass and root exudates

Global nitrogen (N) deposition has a significant impact on the structure and function of above-ground plant communities; however, the impact of N enrichment on below-ground microbial communities remains insufficiently elucidated, especially regarding the functional gene structure. An 18-month pot experiment was conducted to examine the effects of N addition rate (0, 5, 10, and 15 g N m−2 yr−1) on the functional gene composition of rhizosphere microorganisms of Bothriochloa ischaemum, a native grass species of the semiarid area, and to evaluate the soil and plant variables connected with the observed variation. Using microarray GeoChip analysis, 2676, 744, 308, and 515 gene probes involved in carbon (C), N, phosphorus (P) and sulfur (S) cycling, respectively, were detected. Compared with the weak response of genes in the bulk soil, N addition significantly increased the abundance of genes involved in C fixation (tkta, rubisco, TIM), C degradation (amyA, ara, chitinase), methanogenesis (mcra), N2-fixation (nifH), denitrification (narG, nirK/S, nosZ), polyphosphate degradation (ppx), and sulfite reduction (dsrA, dsrB, cysJ) in the rhizosphere. The abundance of genes responsible for C-, N-, P-, and S-cycling increased with the N addition rate and was mainly regulated by variations in plant biomass and root exudates. The quantity of soil dissolved organic C played a crucial role in determining the abundance of genes related to the cycling of C, N, P, and S. Plant biomass indirectly affected gene abundance by increasing organic acids in root exudates and dissolved organic C. These findings facilitate our understanding of microbial function to elevated N levels and highlight the key role of root exudates and plant biomass in regulating microbial functions under future N-enrichment scenarios.

From Biological Gene to Functional Gene: Revolutionizing Product Innovation Design

The functional gene is a product of functional information expression methods inspired by biological genes. Product innovation design is essentially a process of functional problem-solving, which has an intrinsic connection with biological gene expression. The analogy of biological genes, which standardize product function information into functional genes and apply them in product innovation design, holds enormous potential. This paper provides a comprehensive analysis of relevant literature. Firstly, it elaborates on the development of functional genes from the refinement of product genes, clarifying the relationship between functional genes and product genes. Then, it discusses the theoretical foundations of functional gene research, such as the concept, characteristics, and information transmission pathways of functional genes. Moreover, it analyzes key technologies for the application of functional genes, such as functional information encoding forms, and functional gene structure, while summarizing research case studies on functional gene applications. Finally, it explores three key challenges: determining functional gene information content, protecting intellectual property rights, and identifying defects. It also proposes research entry points, aiming to provide references for the field of product innovation design.

Long-term moderate fertilization increases the complexity of soil microbial community and promotes regulation of phosphorus cycling genes to improve the availability of phosphorus in acid soil

Microbial community and functional genes associated with phosphorus (P) cycling are intrinsic to soil P transformation. Yet, how the P fertilization rates affect the interactions of the microbial community and functional genes of P profiles is urgently needed to improve fertilizer P utilization efficiency. To address this, we conducted a long-term field experiment on purple acid soil in southwestern China using five mineral P fertilization rates. We analyzed the amplicon and metagenomic sequencing data to investigate the impact of P application rates on the bacterial and fungal communities as well as P cycling genes. Our results indicate that the community structure of both microbes and functional genes was significantly affected by P fertilization. Compared to other P levels, P application at 33 kg P ha−1 significantly increased the average degree and cohesion in the bacteria-fungi network, while the interactions between P cycling genes and microbes were also complex. Meanwhile, P application up to 16 kg P ha−1 increased the abundance of dominant functional genes (gcd and phoD), which were negatively correlated with Po and Pi. Nocardioides, Candidatus Solibacter, and Gaiella were the dominant taxon that induced the P cycling. The partial least squares path model (PLS-PM) revealed that SOM and pH were the main factors influencing AP by affecting the diversity and cohesion of the bacteria-fungi community, as well as gene abundance of P cycling genes under long-term gradient P fertilization. Overall, these results highlight the potential of moderate P fertilization to promote the stability of the microbiology and P transformation in acid soil.

Global diversity and biogeography of DNA viral communities in activated sludge systems

BackgroundActivated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses that regulate microbial metabolism and nutrient cycling, significantly influencing the stability of AS systems. However, our knowledge about the diversity of viral taxonomic groups and functional traits in global AS systems is still limited. To address this gap, we investigated the global diversity and biogeography of DNA viral communities in AS systems using 85,114 viral operational taxonomic units (vOTUs) recovered from 144 AS samples collected across 54 WWTPs from 13 different countries.ResultsAS viral communities and their functional traits exhibited distance-decay relationship (DDR) at the global scale and latitudinal diversity gradient (LDG) from equator to mid-latitude. Furthermore, it was observed that AS viral community and functional gene structures were largely driven by the geographic factors and wastewater types, of which the geographic factors were more important. Carrying and disseminating auxiliary metabolic genes (AMGs) associated with the degradation of polysaccharides, sulfate reduction, denitrification, and organic phosphoester hydrolysis, as well as the lysis of crucial functional microbes that govern biogeochemical cycles were two major ways by which viruses could regulate AS functions. It was worth noting that our study revealed a high abundance of antibiotic resistance genes (ARGs) in viral genomes, suggesting that viruses were key reservoirs of ARGs in AS systems.ConclusionsOur results demonstrated the highly diverse taxonomic groups and functional traits of viruses in AS systems. Viral lysis of host microbes and virus-mediated HGT can regulate the biogeochemical and nutrient cycles, thus affecting the performance of AS systems. These findings provide important insights into the viral diversity, function, and ecology in AS systems on a global scale.-K8pwvbs3fYC6bGWQ-q_MyVideo

Soil pH dominance over livestock management in determining bacterial assemblages through a latitudinal gradient of European meadows and pastures

Grasslands represent key functional ecosystems due to their global contribution to macronutrients cycling and their role as reservoirs of microbial diversity. The strategic importance of these habitats rests on their involvement in carbon and nitrogen fluxes from the atmosphere to the soil, while at the same time offering extensive sites for livestock rearing. In this study the management type, differentiated in pasture or meadow, was investigated as a variable for its possible effects on overall bacterial diversity and specific genes related to functional guilds. Its contribution was compared to that of other variables such as region, soil pH, and soil organic carbon, to rank their respective hierarchies in shaping microbial community structure. A latitudinal gradient across the European continent was studied, with three sampling groups located in Norway, France, and Northern Italy. The applied methods involved 16S DNA metabarcoding for taxonomic classification and determination of the relative abundance of the bacterial component, and quantitative PCR for the genetic determinants of bacterial and archaeal nitrification, intermediate or terminal denitrification, and nitrogen fixation. Results indicated that soil pH exerted the dominant role, affecting high taxonomy ranks and functions, along with organic carbon and region, with whom it partly covaried. In contrast, management type had no significant influence on microbial community structure and quantitative counts of functional genes. This suggests an ecological equivalence between the impacts of pasture and meadow practices, which are both perturbations that share the aspect of vegetation withdrawal by browsing or cutting, respectively.

Effect of magnetic fields on simultaneous nitrification and denitrification microbial systems.

Magnetic fields positively influence the nitrogen removal efficiency in activated sludge systems. However, the structural succession pattern of microorganisms by magnetic fields still remains further explored. In this paper, a magnetic simultaneous nitrification and denitrification (MSND) reactor was constructed, and the influence of optimized magnetic field intensity (0, 10, 20 and 30 mT) on the nitrogen removal efficiency was investigated at HRT 6 h, 28.0-30.0 °C, and pH 7.0-8.0. Molecular biology was used to investigate the succession process of the dominant microbial flora and the functional gene structure of MSND systems. The results showed that the denitrification effects of the MSND system were significantly enhanced, which contributed to the lower concentration of total nitrogen in the effluent of the magnetic reactor than that of the nonmagnetic group reactor. The magnetic fields induced the succession of microbial community structure and improved the stability of microbial communities, thereby the relative abundances of nitrifying and denitrifying bacteria, and the functional genes were improved. In particular, the abundance of functional genes related to gene proliferation and transmembrane transport was increased. Therefore, the efficient nitrogen removal was achieved, which gives inspiration in the enhanced wastewater treatment by magnetic fields.

Ocean acidification altered microbial functional potential in the Arctic Ocean

AbstractOcean acidification (OA) has considerably changed the metabolism and structure of plankton communities in the ocean. Evaluation of the response of the marine bacterioplankton community to OA is critical for understanding the future direction of bacterioplankton‐mediated biogeochemical processes in the ocean. Understanding the diversity of functional genes is important for linking the microbial community to ecological and biogeochemical processes. However, the influence of OA on the functional diversity of bacterioplankton remains unclear. Using high‐throughput functional gene microarray technology (GeoChip 4), we investigated the functional gene structure and diversity of bacterioplankton under three different pCO2 levels (control: 175 μatm, medium: 675 μatm, and high: 1085 μatm) in a large Arctic Ocean mesocosm experiment. We observed a higher evenness of microbial functional genes under elevated pCO2 compared with under low pCO2. OA induced a more stable community as evaluated by decreased dissimilarity of functional gene structure with increased pCO2. Molecular ecological networks under elevated pCO2 became more complex and stable, supporting the central ecological tenet that complexity begets stability. In particular, increased average abundances were found under elevated pCO2 for many genes involved in key metabolic processes, including carbon degradation, methane oxidization, nitrogen fixation, dissimilatory nitrite/nitrate reduction, and sulfide reduction processes. Altogether, these results indicate a significant influence of OA on the metabolism potential of bacterioplankton in the Arctic Ocean. Consequently, our study suggests that biogeochemical cycling mediated by these microbes may be altered by the OA in the future.

14-3-3ζ Pseudogenes: Physiologically and powerful evolutionary forces in the genome

Abstract Contrary to the rigid dogma ruling out the phenotypic relevance of pseudogenes, recent RNA-seq and meta-analyses indicate that 10% of all pseudogenes are transcribed, and 40% of those pseudogenes are translated into protein. This investigation unpackages the 14-3-3ζ (YWHAZ) gene, which has been shown to regulate cytokine signaling, induce antibody response, and reduce inflammation in rats with rheumatoid arthritis. The original YWHAZ gene is located on the 8 thhuman chromosome. Our detailed investigation in the human genome shows that there are ten pseudogenes of YWHAZ. Located across the human genome, these pseudogenes display unique properties, such as having allelic SNPs for Body Mass Index, Prostatic Neoplasms, and Macular Degeneration. Diverse mRNA expression profiles skewed towards reproductive organs and an unusually high transcription rate (9 of 10 being actively transcribed) suggest a strong physiological relevance. Additionally, contrary to the prevailing pseudogene formation theory where all exons are transcribed, YWHAZ pseudogenes have omitted the sixth exon’s UTR region, resulting in a more compact, equally functional gene structure. The evolution of the YWHAZ pseudogene from the parent gene’s framework, combined with some pseudogenes having allelic properties, demonstrates how pseudogenes may be the body’s way to repackage and repurpose parent genes for a more diverse genome and proteome.

Co-incorporation of Chinese milk vetch (Astragalus sinicus L.) and chemical fertilizers alters microbial functional genes supporting short-time scale positive nitrogen priming effects in paddy soils

Nitrogen (N) priming is a microbially mediated biochemical process as affected by different incorporation practices. However, little information is known about the microbial mechanisms driving the response of N priming to co-operation of Chinese milk vetch (CMV, Astragalus sinicus L.) and different rates of chemical fertilizers in paddy soils in South China. Here, an anaerobic incubation experiment was conducted to study N priming effects (PE) and their relationships with soil microbial functional genes after CMV incorporation alone (M), co-incorporation of CMV with 100% (normal dosage) chemical fertilizers (MC100), and co-incorporation of CMV with 80% chemical fertilizers (MC80). Co-incorporation of CMV and chemical fertilizers enhanced the short-time scale (the first 20 d of incubation) positive PE of N, while no significant differences existed among the three treatments on day 60 or 90 of incubation (P > 0.05). Compared with the M treatment, gross priming effect (GPE) in the MC100 and MC80 treatments significantly increased by 34.0% and 31.3%, respectively, and net priming effect (NPE) increased by 47.7% and 47.8%, respectively, during the first 20 d of incubation (P < 0.05). This was likely attributed to soil nutrient availability and added substrate quality. The MC100 and MC80 treatments increased the gdhA gene abundance by 5.0% and 9.8%, increased the gdh2 gene abundance by 12.7% and 45.7%, and increased the nasB gene abundance by 9.5% and 41.4%, respectively, in comparison with the M treatment on day 20 of incubation. Correlation analyses indicated that soil microbial functional genes involved in N mineralization (gdhA and gdh2), assimilatory nitrate reduction (nasB), and nitrification (amoB) were significantly correlated with N priming under different incorporation practices during the incubation period (P < 0.05). Thus, co-incorporation of CMV and chemical fertilizers can regulate soil microbial community functional gene structure, which may accelerate mineralization and assimilatory nitrate reduction and inhibit nitrification, thereby increasing the short-term positive PE of N in the present study.

Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone.

The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4+ content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.

QMEC-based Analysis of the Soil Microbial Functional Potentials across Different Tibetan Plateau Glacier Forelands

Soil microorganisms dominate the biogeochemical cycles of elements in glacier forelands, which continue to expand due to the climate warming. We analyzed the soil microbial functional characteristics among three types of glacier forelands on the Tibetan Plateau: Yulong Glacier (Y), a temperate glacier; Tianshan Urumqi Glacier No.1 (T), a sub-continental glacier; and Laohugou Glacier No.12 (L), a continental glacier. Here, soil microbial functional genes were quantified using quantitative microbial element cycling technology (QMEC). We found that, in the three glacier forelands, the abundances of soil microbial functional genes related to hemicellulose degradation and reductive acetyl-CoA pathway were highest compared with other carbon-related functional genes. The main nitrogen cycling genes were involved in ammonification. The functional genes of the phosphorus cycle and sulfur cycle were related to organic phosphate mineralization and sulfur oxidation. Furthermore, the soils of the temperate glacier foreland with better hydrothermal conditions had the most complex microbial functional gene structure and the highest functional potentials, followed by those of the soils of continental glacier foreland with the driest environment. These significant differences in soil microbial functional genes among the three types of glacier forelands verified the impacts of geographic difference on microbial functional characteristics, as well as providing a basis for the study of soil microbial functions and biogeochemical cycles in glacier forelands.

Meta-analysis of the effect of nitrification inhibitors on the abundance and community structure of N2O-related functional genes in agricultural soils

Application of nitrification inhibitors (NIs) in agricultural systems is an important strategy to enhance fertilizer nitrogen use efficiency and mitigate soil nitrous oxide (N2O) emissions. Here, we conducted a global meta-analysis of 88 published studies to assess the response of N2O-related functional gene and transcript abundances, and community structure to NIs application. Application of NIs significantly reduced the abundance of ammonia-oxidizing bacteria ammonia monooxygenase (AOB amoA) genes, AOB amoA transcript and nitrite reductase (nirS and nirK) genes. The effectiveness of NIs on reducing the AOB amoA abundance was influenced by N form, soil texture, soil pH and the experimental type (field vs. laboratory). Specifically, NIs were more effective when a mixed inorganic and organic N source was applied to a medium-textured soils. The NIs effectiveness increased with increasing soil pH. The response of AOB amoA abundance to NIs application was not affected by NI type, N rate, soil moisture, soil temperature and soil organic carbon (SOC). The inhibitory effect of NIs on nirS abundance increased with increasing soil temperature. NIs decreased soil nitrifying enzyme activity (NEA) and denitrifying enzyme activity (DEA) by 34.5 % and 27.0 %, respectively, leading to an overall 63.6 % reduction of N2O emissions. Soil NEA correlated positively with the abundance and community structure of AOB amoA but not with AOA amoA. Decrease in DEA with NIs application coincided with the decreasing nirS and nirK abundances. This global-scale assessment demonstrates that the effectiveness of NIs in reducing N2O emissions was attributed to the inhibiting effects on AOB amoA, nirS and nirK genes. Our findings highlight that NIs' inhibition effects on bacterial ammonia-oxidizing community and the encode enzymes in transformation of nitrite to nitric oxide are the main mechanisms for mitigation of N fertilizer-induced N2O emissions.

Humic Lake Exhibits Higher Microbial Functional Gene Diversity and Weaker Gene Interaction Efficiency than a Common Alkaline Lake.

Simple SummaryThe humic lake represents a special kind of aquatic ecosystem with high humic substances, low irradiance, and a high potential for greenhouse gas emissions. Despite the special environment and biogeochemical processes in humic lake water, knowledge about the underlying microbial-driven functions remains elusive. Here, we studied the compositions and functional gene structures of microbial communities in a humic lake (HL) and a reference weakly alkaline lake (RAL). We found that the high organic matter content in the HL supported higher gene diversity; and, specifically, the carbon and nitrogen fixations, the degradation of various types of carbon, methane oxidation and methanogenesis, ammonification, denitrification, and assimilatory N reduction might be enhanced more in the HL than in the RAL. By contrast, the humic fractions in the HL might reduce microbial metabolic potential for sulfur oxidation and phosphorus degradation. The potential interactions between different functional microorganisms might be down-regulated provided that there were more easily acquired nutrients in the HL. Overall, our results showed the functional gene “landscape” of microbial communities in the surface water of a humic lake, which helps understand the biogeochemical processes and the remediation of organic matter pollution in lacustrine ecosystems.Humic lakes (HLs) are special water bodies (high organic matter content, low pH, and low transparency) that are important sources of major greenhouse gases. The knowledge about microbial functional potentials and the interactions among different genes in HL water has been scarcely understood. In this study, we used 16S rRNA gene sequencing and the GeoChip 5.0 to investigate microbial community compositions and functional gene structures in an HL and a reference weakly alkaline lake (RAL). The HL microbial communities showed distinct compositions and functional gene structures than those in the RAL. The functional gene diversity was significantly higher in the HL than in the RAL. Specifically, higher gene relative intensities in carbon and nitrogen fixations, the degradation of various types of carbon, methane oxidation and methanogenesis, ammonification, denitrification, and assimilatory N reduction were observed in the HL samples. By contrast, the metabolic potentials of microorganisms involved in dissimilatory N reduction, phosphorus degradation, and sulfur oxidation were weaker in the HL than in the RAL. Despite higher functional gene diversity, the interaction efficiency among genes (reflected by network geodesic distance and clustering coefficient) might be reduced in the HL. Different functional microbes may develop less interdependent relationships in acquiring nutrients given the high resource availability in the HL. Overall, the enhanced microbial metabolic potentials and less efficient functional interactions might have great consequences on nutrient cycling and greenhouse gas emissions in the HL ecosystem.

Insights into sweet potato SR proteins: from evolution to species-specific expression and alternative splicing.

SR proteins from sweet potato have conserved functional domains and similar gene structures as that of Arabidopsis and rice in general. However, expression patterns and alternative splicing regulations of SR genes from different species have changed under stresses. Novel alternative splicing regulations were found in sweet potato SR genes. Serine/arginine-rich (SR) proteins play important roles in plant development and stress response by regulating the pre-mRNA splicing process. However, SR proteins have not been identified so far from an important crop sweet potato. Through bioinformatics analysis, our study identified 24 SR proteins from sweet potato, with comprehensively analyzing of protein characteristics, gene structure, chromosome localization, and cis-acting elements in promotors. Salt, heat, and mimic drought stresses triggered extensive but different expressional regulations on sweet potato SR genes. Interestingly, heat stress caused the most active disturbances in both gene transcription and pre-mRNA alternative splicing (AS). Tissue and species-specific transcriptional and pre-mRNA AS regulations in response to stresses were found in sweet potato, in comparison with Arabidopsis and rice. Moreover, novel patterns of pre-mRNA alternative splicing were found in SR proteins from sweet potato. Our study provided an insight into similarities and differences of SR proteins in different plant species from gene sequences to gene structures and stress responses, indicating SR proteins may regulate their downstream genes differently between different species and tissues by varied transcriptional and pre-mRNA AS regulations.

Microbial biodiversity contributes to soil carbon release: a case study on fire disturbed boreal forests.

Microbial communities often possess enormous diversity, raising questions about whether this diversity drives ecosystem functioning, especially the influence of diversity on soil decomposition and respiration. Although functional redundancy is widely observed in soil microorganisms, evidence that species occupy distinct metabolic niches has also emerged. In this paper, we found that apart from the environmental variables, increases in microbial diversity, notably bacterial diversity, lead to an increase in soil C emissions. This was demonstrated using structural equation modelling (SEM), linking soil respiration with naturally differing levels of soil physio-chemical properties, vegetation coverage, and microbial diversity after fire disturbance. Our SEMs also revealed that models including bacterial diversity explained more variation of soil CO2 emissions (about 45%) than fungal diversity (about 38%). A possible explanation of this discrepancy is that fungi are more multifunctional than bacteria and, therefore, an increase in fungal diversity does not necessarily change soil respiration. Further analysis on functional gene structure suggested that bacterial and fungal diversities mainly explain the potential decomposition of recalcitrant C compare with that of labile C. Overall, by incorporating microbial diversity and the environmental variables, the predictive power of models on soil C emission was significantly improved, indicating microbial diversity is crucial for predicting ecosystem functions.

Domesticating a bacterial consortium for efficient lignocellulosic biomass conversion

Microbial consortia-based consolidated bioprocessing (CBP) is a promising trend in biomass biorefinery, but still faces challenges in terms of complicated microbial structure, low conversion efficiency and operation instability. This study constructed an artificial consortium with improved biomass conversion capability and good operation stability. Diversity of the microbial community structure and gene functions of the domesticated consortium was then analyzed, finding that it had a simplified microbial structure and aggregation of functional genes related to conversion of cellulosic materials for biofuel production. Finally, CBP of wheat straw was performed using the domesticated consortium, ethanol and solvent production with the highest yield ever reported at 0.37 g/g and 0.60 g/g respectively were achieved. Our results further highlight the potential of this domesticated consortium in lignocellulosic biomass biorefinery in comparison with previously reported microbial consortia. Overall, this study provides a guidance on the artificial construction of simplified functional consortia for producing valuable chemicals in a sustainable way.

Meta-Analysis of the Effect of Nitrification Inhibitors on the Abundance and Community Structure of N2o-Related Functional Genes in Agricultural Soils

Meta-Analysis of the Effect of Nitrification Inhibitors on the Abundance and Community Structure of N2o-Related Functional Genes in Agricultural Soils