Functional Gene Composition Research Articles

The effects of nitrogen addition on soil organic carbon decomposition and microbial C-degradation functional genes abundance in a Pinus tabulaeformis forest

Nitrogen (N) deposition affects soil organic carbon (SOC) decomposition, therefore altering the global terrestrial carbon (C) cycle. However, it remains unclear how N deposition affects SOC decomposition by regulating microbial community composition and function, especially C-cycling functional gene composition. We investigated the effects of N addition (0, 3, 6, and 9 g N m−2y–1) on the composition of soil microbial C-cycling functional gene, SOC-degrading enzyme activities, and CO2 emissions in a Pinus tabulaeformis forest. Under low N addition (3 or 6 g N m−2y–1), labile C-degradation gene abundances were significantly increased. Under high N addition (9 g N m−2y–1), C-cycling functional gene abundance and diversity were significantly decreased. These effects were related to the changes in soil NO3–-N, dissolved organic C, total N, and microbial biomass C contents. Furthermore, low N addition stimulated the activities of SOC-degrading enzyme and CO2 emissions, whereas high N addition had the inhibitory effect. C-degradation gene abundances were significantly correlated with the SOC-degrading enzyme activities and CO2 emissions. Increase in CO2 emission rates were related to the high microbial functional potentials for labile C degradation under low N addition, whereas the lower CO2 emission rates were related to the low microbial functional potentials for labile as well as recalcitrant C degradation under high N addition. Our study indicated that N deposition may change SOC decomposition by altering the abundance of labile C and recalcitrant C degradation genes.

Phenanthrene degradation in soil using biochar hybrid modified bio-microcapsules: Determining the mechanism of action via comparative metagenomic analysis

A strategy involving biochar (BC) hybrid modification was developed to promote the bioremediation effect of degrading bacteria immobilized in layer-by-layer assembly (LBL) microcapsules for the treatment of phenanthrene (PHE) polluted soil. A taxonomic and functional metagenomic approach was used to investigate changes in the microbial community structures and functional gene compositions in the PHE-polluted soil during the bioremediation process. Biofortification with an initial PHE concentration of 100 mg kg−1 dry soil in soils using the BC (3%) hybrid LBL bio-microcapsule (BC-LBL, 2.0 g kg−1 dry soil, 107 colony forming unite cell g−1 dry soil) was faster; further, a higher PHE degradation efficiency (80.5% after 25 d) was achieved when compared with that by the LBL agent (66.2% after 25 d) used. Sphingomonas, Streptomyces, Gemmatirosa, Ramlibacter, Flavisolibacter, Phycicoccus, Micromonospora, Acidobacter, Mycobacterium and Gemmatimonas were more abundant in BC-LBL treatment than those in LBL one. Functional gene annotation results showed that more gene number with BC-LBL treatment than those with LBL one. More abundant functions in the former were primarily related to the growth, reproduction, metabolism, and transportation of bacteria. BC hybridization promoting PHE degradation by microencapsulated bacteria may be due to the strong adsorption property of BC, which results in the enrichment of the nutrients that needed for bacterial growth and reproduction, as well as enhancing the mass transfer performance of PHE to BC-LBL; Meanwhile, BC could also stimulate and improve the metabolism and membrane transportation of the degrading bacteria, and finally improving the degradation function.

Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition

Climate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.0) to analyze taxonomic and functional gene compositions of the soil microbial community after 14 years of warming (at 0.8–1.0 °C for 10 years and then 1.5–2.0 °C for 4 years) in a Californian grassland. Long-term warming had no detectable effect on the taxonomic composition of soil bacterial community, nor on any plant or abiotic soil variables. In contrast, functional gene compositions differed between warming and control for bacterial, archaeal, and fungal communities. Functional genes associated with labile carbon (C) degradation increased in relative abundance in the warming treatment, whereas those associated with recalcitrant C degradation decreased. A number of functional genes associated with nitrogen (N) cycling (e.g., denitrifying genes encoding nitrate-, nitrite-, and nitrous oxidereductases) decreased, whereas nifH gene encoding nitrogenase increased in the warming treatment. These results suggest that microbial functional potentials are more sensitive to long-term moderate warming than the taxonomic composition of microbial community.

Bacterial communities and functional genes stimulated during phenanthrene degradation in soil by bio-microcapsules

In this study, a taxonomic and functional metagenomic method was used to investigate the difference produced between degrading bacteria immobilized in layer-by-layer assembly (LBL) microcapsules or not during the bioremediation of a soil polluted with phenanthrene (PHE). Bioaugmentation with LBL microcapsule immobilized degrading bacteria could result in different changes of native microbial communities, shifting the functional gene constructions of polluted soils. The LBL treatment enhanced PHE degradation (initial concentration of 100 mg kg−1 dry soil) by 60% after 25 d compared to the free bacteria (FB). The enhancing effect of PHE degradation produced by the LBL treatment was found to be significantly associated with some crucial phyla (e.g., Bacteroides, Gemmatimonadetes and Acidobacteria) and genera including Streptomyces, Ramlibacter, Mycobacterium, Phycicoccus, Gemmatirosa, Flavisolibacter, Micromonospora, Acid_Candidatus_Koribacter and Gemmatimonas. The main differences of functional metagenomics between LBL and FB treatments were observed in higher levels in metabolism of aromatic hydrocarbons and its related functions or enzymes in the former, e.g., membrane transport systems, binding, substrate transporter, cleavage enzymes, dehydrogenation, oxidase, esterase and glycosidase, greatly favoring PHE mineralization. Therefore, our results provide useful findings on understanding of how immobilization strategies can influence the taxonomic and functional gene composition in soils, as well as polycyclic aromatic hydrocarbons (PAH) degradation.

Low N2O emissions from wheat in a wheat-rice double cropping system due to manure substitution are associated with changes in the abundance of functional microbes

Fertilization has been shown to affect nitrogen (N) cycling and its related functional microbes in agricultural soils. However, the linkage between soil N2O emissions and N-related functional genes under different fertilization strategies from wheat in a wheat-rice double cropping system is rarely examined. Here, we carried out a two-year field study to examine the response of soil N2O emissions driven by N cycling functional genes [archaeal and bacterial amoA (AOA + AOB), nirS, nirK and nosZ] to different fertilization strategies in a wheat cropland of subtropical China. Three fertilizer treatments were established consisting of chemical phosphorus (P) and potassium (K) fertilizer application (PK), chemical N (urea) and PK fertilizer application (NPK), and chemical NPK fertilizer application with chemical N partially replaced with manure (composted pig manure) (NPKM). Over the two wheat seasons, seasonal total N2O emissions averaged 0.66, 3.60 and 3.11 kg N ha−1 for PK, NPK and NPKM plots, respectively. Relative to the NPK treatment, the NPKM treatment significantly decreased N2O emissions by 14 % without compromising grain yield, with a lowered combined fertilizer-induced emission factor (EF) of 1.02 %. Compared with the PK treatment, N fertilization consistently and significantly increased the abundance of ammonium-oxidation bacteria (AOB), nirS, nirK and nosZ genes. The nosZ gene, which drives N2O reduction during denitrification, showed a greater extent under NPKM with manure N combination. The AOB had a more sensitive response than ammonium-oxidation archaea (AOA) to chemical N fertilization. Seasonal N2O emissions showed significant positive correlations with AOB gene abundance and the ratio of (nirK+nirS)/nosZ, while had a negative correlation with nosZ gene abundance across N fertilized treatments. The N2O-related microbial composition of functional genes was significantly changed by N fertilizer application and also showed contrasting patterns between treatments of chemical N fertilizer with and without manure N substitution. Together, partially replacing chemical N fertilizer with manure reduced N2O emissions from wheat in a wheat-rice double cropping system, mainly through decreasing AOB associated-nitrifying potential, and particularly stimulating N2O reduction.

Soil aggregate size-dependent relationships between microbial functional diversity and multifunctionality

Soil stability and aggregates are important drivers of soil fertility and microbial diversity and are highly vulnerable to land degradation. However, the role of soil aggregates in driving the responses of microbial functional diversity and multiple ecosystem services and functions (multifunctionality) to further degradation (e.g., fertilization) remains largely unexplored and poorly understood. In this study, we used soils from long-term experiments involving inorganic and organic fertilization treatments to investigate the role soil aggregates (microscale) play in driving microbial functional gene diversity (via GeoChip) and the activity of multiple extracellular enzymes in an agricultural ecosystem. We found that microbial functional gene diversity has a significant and positive relationship with soil multifunctionality, which is enhanced in soil aggregates by organic fertilizer but is reduced by inorganic fertilizer. We also found that soil aggregate fractions indirectly controlled multiple ecosystem functions via changes in functional diversity. Smaller soil aggregates with higher resource availability (carbon and nitrogen) supported more ecological functions than larger aggregates under contrasting fertilizer management regimes. Soil multifunctionality is regulated by the differences in resource availability and not by microbial functional gene composition, which suggests that microbial functional diversity contributed more to multifunctionality than gene composition. Random forest analysis and structural equation modeling indicated that soil carbon and nitrogen and microbial functional diversity together determined the multifunctionality, whereas soil traits have more standardized total effects than functional diversity. Our study highlights that soil aggregation stratifies soil nutrition and microbial functional diversity, which leads to the differentiation of aggregate ecosystem multifunctionality.

The Gut Microbiome Is Altered in Postmenopausal Women With Osteoporosis and Osteopenia.

ABSTRACTOsteoporosis and its precursor osteopenia are common metabolic bone diseases in postmenopausal women. A growing body of evidence suggests that the gut microbiota is involved in the regulation of bone metabolism; however, there are few studies examining how gut microbiomes in osteoporosis and osteopenia may differ from those in healthy individuals. The aim of this study was to characterize the diversity, composition, and functional gene potential of the gut microbiota of healthy, osteopenic, and osteoporotic women. Body composition, bone density, and fecal metagenomes were analyzed in 86 postmenopausal women. The women were classified as healthy, osteopenic, or osteoporotic based on T‐scores. The taxonomic and functional gene compositions of the microbiome were analyzed using shotgun metagenomic sequencing. Both osteoporotic and osteopenic taxonomic compositions were found to be significantly different from healthy participants. Linear discriminant‐analysis effect‐size analyses identified that healthy participants had more unclassified Clostridia and methanogenic archaea (Methanobacteriaceae) than in both osteoporotic and osteopenic participants. Bacteroides was found to be more abundant in osteoporosis and osteopenia groups. Some KEGG pathways, including carbohydrate metabolism, biosynthesis of secondary metabolites, and cyanoamino acid metabolism, were found to be more abundant in both osteoporosis and osteopenia. These results show that osteoporosis and osteopenia alter the gut microbiome of postmenopausal women and identify potential microbial taxonomic and functional pathways that may be involved in this disease. © 2020 The Authors. JBMR Plus published by Wiley Periodicals LLC. on behalf of American Society for Bone and Mineral Research.

Soil Microbial Composition and phoD Gene Abundance Are Sensitive to Phosphorus Level in a Long-Term Wheat-Maize Crop System.

Microbes associated with phosphorus (P) cycling are intrinsic to soil P transformation and availability for plant use but are also influenced by the application of P fertilizer. Nevertheless, the variability in soil P in the field means that integrative analyses of soil P cycling, microbial composition, and microbial functional genes related to P cycling remain very challenging. In the present study in the North China Plain, we subjected the bacterial and fungal communities to amplicon sequencing analysis and characterized the alkaline phosphatase gene (phoD) encoding bacterial alkaline phosphatase in a long-term field experiment (10 years) with six mineral P fertilization rates up to 200 kg P ha–1. Long-term P fertilization increased soil available P, inorganic P, and total P, while soil organic P increased until the applied P rate reached 25 kg ha–1 and then decreased. The fungal alpha-diversity decreased as P rate increased, while there were no significant effects on bacterial alpha-diversity. Community compositions of bacteria and fungi were significantly affected by P rates at order and family levels. The number of keystone taxa decreased from 10 to 3 OTUs under increasing P rates from 0 to 200 kg ha–1. The gene copy numbers of the biomarker of the alkaline phosphatase phoD was higher at moderate P rates (25 and 50 kg ha–1) than at low (0 and 12.5 kg ha–1) and high (100 and 200 kg ha–1) rates of P fertilization, and was positively correlated with soil organic P concentration. One of the keystone taxa named BacOTU3771 belonging to Xanthomonadales was positively correlated with potential functional genes encoding enzymes such as glycerophosphoryl diester phosphodiesterase, acid phosphatase and negatively correlated with guinoprotein glucose dehydrogenase. Altogether, the results show the systematic effect of P gradient fertilization on P forms, the microbial community structure, keystone taxa, and functional genes associated with P cycling and highlight the potential of moderate rates of P fertilization to maintain microbial community composition, specific taxa, and levels of functional genes to achieve and sustain soil health.

Land-use change from cropland to plantations affects the abundance of nitrogen cycle-related microorganisms and genes in the Loess Plateau of China

The “Grain for Green” project has been considered an effective avenue to control soil erosion, improve vegetation coverage and prevent ecosystem degradation in the Loess Plateau of China. However, the effect of the project on the underlying microbial mechanism of soil nitrogen cycling is not well understood. In the present study, the effect of land-use change from cropland to plantations on soil microbial community and functional genes involved in the nitrogen cycle was investigated via metagenomic sequencing analyses. The abundance rather than the composition of functional genes for nitrification, denitrification, assimilatory and dissimilatory nitrogen reduction significantly changed during the conversion of cropland to plantations. The abundance rather than the composition of microorganisms involved in the nitrogen cycle also changed significantly. The effect on the abundance of functional genes and microorganisms was mainly related to changes in soil properties, such as organic matter, total nitrogen, available phosphorus, available potassium and pH. The observed changes likely decrease the potential of nitrification, denitrification and assimilatory nitrogen reduction in the soil of plantations. Our results demonstrate that land-use change from cropland to plantations significantly affects soil nitrogen cycling in the Loess Plateau of China.

Soil Biogeochemical Cycle Couplings Inferred from a Function-Taxon Network.

Soil biogeochemical cycles and their interconnections play a critical role in regulating functions and services of environmental systems. However, the coupling of soil biogeochemical processes with their mediating microbes remains poorly understood. Here, we identified key microbial taxa regulating soil biogeochemical processes by exploring biomarker genes and taxa of contigs assembled from metagenomes of forest soils collected along a latitudinal transect (18° N to 48° N) in eastern China. Among environmental and soil factors, soil pH was a sensitive indicator for functional gene composition and diversity. A function-taxon bipartite network inferred from metagenomic contigs identified the microbial taxa regulating coupled biogeochemical cycles between carbon and phosphorus, nitrogen and sulfur, and nitrogen and iron. Our results provide novel evidence for the coupling of soil biogeochemical cycles, identify key regulating microbes, and demonstrate the efficacy of a new approach to investigate the processes and microbial taxa regulating soil ecosystem functions.

Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stability.

High-latitude tundra ecosystems are increasingly affected by climate warming. As an important fraction of soil microorganisms, fungi play essential roles in carbon degradation, especially the old, chemically recalcitrant carbon. However, it remains obscure how fungi respond to climate warming and whether fungi, in turn, affect carbon stability of tundra. In a 2-year winter soil warming experiment of 2°C by snow fences, we investigated responses of fungal communities to warming in the active layer of an Alaskan tundra. Although fungal community composition, revealed by the 28S rRNA gene amplicon sequencing, remained unchanged (p>.05), fungal functional gene composition, revealed by a microarray named GeoChip, was altered (p<.05). Changes in functional gene composition were linked to winter soil temperature, thaw depth, soil moisture, and gross primary productivity (canonical correlation analysis, p<.05). Specifically, relative abundances of fungal genes encoding invertase, xylose reductase and vanillin dehydrogenase significantly increased (p<.05), indicating higher carbon degradation capacities of fungal communities under warming. Accordingly, we detected changes in fungal gene networks under warming, including higher average path distance, lower average clustering coefficient and lower percentage of negative links, indicating that warming potentially changed fungal interactions. Together, our study reveals higher carbon degradation capacities of fungal communities under short-term warming and highlights the potential impacts of fungal communities on tundra ecosystem respiration, and consequently future carbon stability of high-latitude tundra.

Forest conversion alters the structure and functional processes of tropical forest soil microbial communities

AbstractMany studies have been carried‐out on the effects of forest conversion on soil microbial community composition and diversity. However, impacts on soil microbial functions and how diversity changes across scales are poorly understood. To fill the research gap, we used metagenomic sequencing and 16S rRNA and ITS gene sequences to evaluate the microbial composition, diversity, and function of 260 soil samples collected from tropical rainforest and rubber plantation sites across Hainan Island, South China. The results revealed that: (a) Forest conversion resulted in shifts in microbial composition (from the Proteobacteria to Chloroflexi), archaeal composition (from Thaumarchaeota to Bathyarchaeota), and fungal composition (from Basidiomycota to Ascomycota). (b) Bacterial alpha, beta, and gamma diversity were not reduced by forest conversion. However, fungal beta diversity was lower in the plantations, resulting in a decrease in gamma diversity. Archaeal beta diversity was higher in rainforest versus rubber plantation soils, but archaeal gamma diversity showed the opposite pattern. (c) Soil functional composition and diversity did not differ with forest type; however, genes related to metabolism and degradation processes were significantly more abundant in the tropical rainforest. These changes in gene abundance could alter ecosystem processes. (d) Soil pH and environmental heterogeneity were the main drivers of microbial taxonomic composition and functional gene composition. Land use explained 13.28% of the variation in taxonomic composition but did not explain changes in functional gene composition. We concluded that land use changes can alter soil microbial community structure and have profound effects on ecosystem functions and processes.

Bacterial community diversity of shilixiang baijiu Daqu based on metagenomics.

Daqu is a fermentative saccharifying agent that is used to initiate fermentation in the production of Chinese baijiu. In this study, we performed metagenomic analysis of microorganisms present in shilixiang baijiu Daqu in order to analyze the bacterial community diversity of shilixiang baijiu Daqu from four different fermentation batches and determine the effect of fermentation process on microorganisms. An understanding of the composition and structure of bacterial communities of the shilixiang baijiu Daqu can provide a theoretical basis for the stability and quality evaluation of shilixiang baijiu Daqu-making technology. The results showed that the microbial community structure was different among Daqu samples from different fermentation batches, and at different fermentation days within the same fermentation batch. In general, the abundance and diversity of microorganisms found in Daqu samples from the four batches increased after 30days of fermentation. The analysis of community structure showed that after 30days of fermentation, Firmicutes was the predominant phylum in the four batches of the shilixiang baijiu Daqu samples. After 30days of fermentation, the proportion of Lactobacillus, Pediococcus, and Staphylococcus increased, while the proportion of Pseudomonas decreased; Lactobacillus was the dominant microorganism in the shilixiang baijiu Daqu samples. We also determined that Lactobacillus, Pseudomonas, Leuconostoc, Lactococcus, Saccharopolyspora, and Enterococcus were present in Jannanchun, Maotai, and shilixiang baijiu Daqu samples. In addition, every batch had its own unique genus. We discovered genera that had not been found before in shilixiang baijiu Daqu samples. Through the prediction of functional gene composition, we confirmed that the bacterial population in shilixiang baijiu Daqu mainly had metabolic, genetic information processing, and environmental information processing functions. This study contributes to expanding our understanding of the functional characteristics of Daqu bacterial communities and provides new ideas for future in-depth studies of the diversity and functionality of Daqu bacteria. PRACTICAL APPLICATIONS: This study contributes to expanding our understanding of the functional characteristics of Daqu bacterial communities and provides new ideas for future in-depth studies of the diversity and functionality of Daqu bacteria. Based on these results, we can further select functional strains related to the performance of koji. The results of this study point out the direction for future studies on the formation mechanism of trace aroma substances in baijiu and the improvement of koji quality.

Microbial functional gene diversity in natural secondary forest Ultisols

The diversity and biogeography of functional genes at a regional scale remains unclear. We hypothesize that plant community composition, nutrient availability, and spatial distance are driving factors for the functional gene diversity of soil microorganisms at a regional scale. We also hypothesize that different functional genes have different responses to environment. Using functional gene arrays (GeoChip 3.0), we examined microbial diversity, and influencing factors in Ultisols in 11 natural secondary forest plots in southern China which contained 4073 functional genes averagely. Carbon and nitrogen cycle genes were more variable than genes involved in phosphorus utilization, organic remediation, and metal resistance, in similar trends with soil substrate availability. Genes involved in nitrification being more variable than other nitrogen cycling genes; phytase genes being more variable than polyphosphate kinase genes (ppk) and exopolyphosphatase genes (ppx); exoglucanase and endoglucanase genes being more variable than cellobiase genes; lignin peroxidase genes (lip) being more variable than manganese peroxidase genes (mnp). Approximately 41% of the variation in gene composition could be explained by fine root surface area, available nitrogen, and the largest spatial scale factor, with the former two environmental factors over influenced spatial distance. Both environmental factors (represented by nutrient availability) and spatial distance influenced microbial functional gene composition, while the influence of spatial distance worked through environmental factors in natural secondary forest in Ultisols within approximately 500 km, providing insights into microbial biogeography from a functional gene perspective.

Application of biogas slurry rather than biochar increases soil microbial functional gene signal intensity and diversity in a poplar plantation

Microbes play critical roles in the cycling of nutrients in forest ecosystems. Many studies have shown that the application of organic fertilizer can alter bacterial diversity; however, the responses of soil microbial functional genes to organic fertilization (particularly biogas slurry fertilization, or in combination with biochar) have not been elucidated as yet. We examined the responses of the abundance, diversity, and composition of soil microbial functional genes under five-years of fertilization. This fertilization involved low and high application rates of biogas slurry, at 250 and 375 m3 ha−1 yr−1, respectively, or in combination with low and high application rates of biochar, at 80 and 120 t ha−1, respectively, in a coastal poplar plantation of Eastern China. Compared to the control, the normalized signal intensity of genes in the major functional categories increased significantly in response to the quantity of applied biogas slurry, but insignificantly in response to the additional application of biochar. Subsequent to the application of biogas slurry, the functional gene evenness and Shannon index increased significantly; however, the addition of biochar to the biogas slurry had insignificant effects on the α-diversity of functional genes. These functional gene compositions under five different treatments were well distinguished, primarily through the application of biogas slurry. Our results revealed that the abundance of a large number of key functional genes involved in C, N, and P cycling were effectively increased, and these changes were well correlated with most soil properties. This study reveals the molecular level mechanisms that promote plant growth following organic fertilizer application, through the enhancement of soil microbial functional gene diversity.

C:N ratio is not a reliable predictor of N2O production in acidic soils after a 30-day artificial manipulation

To test the effect of C:N ratio on soil N2O production, N2O production rates and pathways associated with nitrification (AOA-amoA, AOB-amoA, fungal ITS rDNA, bacterial 16S rRNA), and denitrification-related (nirK, nirS, nosZ) genes were investigated in subtropical forest (SF) and cropland (SC) soil in China in a 30-day C:N ratio manipulation. In addition, 24-hour C:N ratio manipulation, including the addition of acetic acid, were conducted to verify the results observed in the 30-day experiment. After 30 days of manipulation, the N2O production rates (N2Ot) increased from 2.46 in CN23 treatment to 4.71 μg N kg−1 day−1 in CN 10 treatment in SF, while it decreased from 4.17 in CN23 treatment to 3.83 μg N kg−1 day−1 in CN10 treatment in SC. The results in 24-hour experiment were consistent with those in 30-day experiment, and the addition of acetic acid increased N2Ot in SC, but not in SF. Soil C:N ratios and inorganic N (NH4+ + NO3−) concentrations influenced the contribution of denitrification to N2O production and the N2O production rate via denitrification. Soil AOA played a dominant role in autotrophic nitrification-derived N2O production, resulting in a high contribution of autotrophic nitrification under low pH. Therefore, pH instead of C:N ratio, is a key parameter for evaluating autotrophic nitrification-derived N2O via AOA and AOB. Soil C:N ratio was significantly and positively correlated with the contribution of heterotrophic nitrification to N2O production, while there was no significant correlation with the N2O production rate via heterotrophic nitrification. This is mainly because the responsible heterotrophs (i.e., fungi and bacteria) were negatively and positively correlated with C:N ratio in SF and SC, respectively. Therefore, C:N ratio is not a strong predictor of soil N2O production, the initial C or N content and composition of functional genes could provide key information in acidic soils after a 30-day artificial C:N ratio manipulation.

Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication.

BackgroundWith the development of DNA sequencing technology, static omics profiling in microbial communities, such as taxonomic and functional gene composition determination, has become possible. Additionally, the recently proposed in situ growth rate estimation method allows the applicable range of current comparative metagenomics to be extended to dynamic profiling. However, with this method, the applicable target range is presently limited. Furthermore, the characteristics of coverage depth during replication have not been sufficiently investigated.ResultsWe developed a probabilistic model that mimics coverage depth dynamics. This statistical model explains the bias that occurs in the coverage depth due to DNA replication and errors that arise from coverage depth observation. Although our method requires a complete genome sequence, it involves a stable to low coverage depth (>0.01×). We also evaluated the estimation using real whole-genome sequence datasets and reproduced the growth dynamics observed in previous studies. By utilizing a circular distribution in the model, our method facilitates the quantification of unmeasured coverage depth features, including peakedness, skewness, and degree of density, around the replication origin. When we applied the model to time-series culture samples, the skewness parameter, which indicates the asymmetry, was stable over time; however, the peakedness and degree of density parameters, which indicate the concentration level at the replication origin, changed dynamically. Furthermore, we demonstrated the activity measurement of multiple replication origins in a single chromosome.ConclusionsWe devised a novel framework for quantifying coverage depth dynamics. Our study is expected to serve as a basis for replication activity estimation from a broader perspective using the statistical model.

Partial function prediction of sulfate-reducing bacterial community from the rhizospheres of two typical coastal wetland plants in China

Sulfate-reducing bacteria (SRB) are ubiquitous anaerobic microorganisms that play significant roles in the global biogeochemical cycle. Coastal wetlands, one of the major habitats of SRB, exhibit high sulfate-reducing activity and thus play significant roles in organic carbon remineralization, benthic geochemical action, and plant-microbe interactions. Recent studies have provided credible evidence that the functional rather than the taxonomic composition of microbes responds more closely to environmental factors. Therefore, in this study, functional gene prediction based on PacBio single molecular real-time sequencing of 16S rDNA was applied to determine the sulfate-reducing and organic substrate-decomposing activities of SRB in the rhizospheres of two typical coastal wetland plants in North and South China: Zostera japonica and Scirpus mariqueter. To this end, some physicochemical characteristics of the sediments as well as the phylogenetic structure, community composition, diversity, and proportions of several functional genes of the SRB in the two plant rhizospheres were analyzed. The Z. japonica meadow had a higher dissimilatory sulfate reduction capability than the S. mariqueter-comprising saltmarsh, owing to its larger proportion of SRB in the microbial community, larger proportions of functional genes involved in dissimilatory sulfate reduction, and the stronger ability of the SRB to degrade organic substrates completely. This study confirmed the feasibility of applying microbial community function prediction in research on the metabolic features of SRB, which will be helpful for gaining new knowledge of the biogeochemical and ecological roles of these bacteria in coastal wetlands.

Soil quality shapes the composition of microbial community stress response and core cell metabolism functional genes

The capacity for soils to perform vital functions, such as agricultural production, is dependent on numerous properties. Their simultaneous effect on soil biota is of interest to assess impacts of agricultural management. Using a soil quality index (SQI) based on a priori assumptions of eight soil physico-chemical properties that promote plant growth and microbial biomass, we sought to: 1) investigate the effect of land use on SQI; and 2) test a relationship between SQI and the composition of microbial functional genes. In 29 soils under four distinct land uses (cotton, wheat, pasture and native vegetation) gene composition was most distinct in cotton. The SQI followed the gradient cotton < wheat < native vegetation < pasture, with pasture significantly greater than other land uses. Of 67 functional gene markers, gradient boosted machine learning identified five genes that correlated strongly with SQI. These were stress response (oxyR and dnaJ), core carbon, nitrogen and sulfur metabolism (PTS-Glc-EIIA, glnH and sat, respectively). Nutrient cycling functional genes did not correlate with SQI. A structural equation model of the relationship between soil properties, SQI, and the aforementioned genes was used to visualise these interactions (root mean squared error of 0.1, R2 of 0.64 and p < 0.001). We conclude that certain land use practices improve or degrade soil quality relative to native vegetation, and SQI primarily correlates with microbial stress response and core metabolism. This demonstrates capacity for microbial communities to adapt to environmental stress while certain functions remain relatively resilient.

2580. Serial Microbiome Analysis in a Patient with Multiple Failed Fecal Microbiome Transplantations

BackgroundFecal microbiota transplantation (FMT) is recommended to treat refractory or recurrent cases of Clostridioides difficile infection (CDI) through restoration of a healthy intestinal microbiome. The procedure has reported success rates of 90% or higher for CDI, but several risk factors for FMT failure have been identified. Here we present a case of a patient failing four FMT procedures over a 2-year period, with accompanying microbiome and metagenomic analyses.MethodsSeven serial C. difficile-positive stool samples were collected as part of an ongoing surveillance system in Texas. Samples, including the index case, represented independent CDI episodes interspersed between four separate FMT procedures between 2016 and 2018. PCR ribotype (RT) testing, 16S rRNA gene sequencing, MIC testing, multidrug-resistant organism (MDRO) screening, and shotgun metagenome sequencing were conducted for each of the samples.ResultsThe patient was a 42-year-old female with various comorbidities, including systemic lupus erythematosus. She received continuous non-CDI antibiotic courses throughout her CDI therapy for a variety of infections. The vancomycin MICs in infecting C. difficile strains increased with cumulative vancomycin exposure. Multidrug-resistant organisms were detected in stool, including Enterococcus spp., MRSA, and Candida glabrata. The first five of the seven strains were RT 078–126, one was mixed RT 002 and RT 054, and one was RT 002. The analysis of 16S rRNA gene sequences demonstrated that microbial diversity was never restored after FMT procedures. A strong correlation between microbial and functional gene compositions suggests that fecal samples share many microbial species with associated functional genes.ConclusionA number of systems biology changes were observed in a patient with persistent CDI despite multiple FMTs. The lack of FMT engraftment was most likely due to continuous broad-spectrum antibiotic exposure in an immunocompromised patient.Disclosures All authors: No reported disclosures.