Effect of soil horizon stratigraphy on the microbial ecology of alpine paleosols

Effects of forest age and season on soil microbial communities in Chinese fir plantations

Understanding changes in the distribution patterns and diversity of soil microbial communities from the perspectives of age-related changes, seasonal variations, and the interaction between the two factors can facilitate the management of plantations. In Chinese fir plantations, we collected soils from different depths in over-mature forests, mature forests, near-mature forests, middle-aged forests, and young forests in summer, autumn, and winter in China's subtropical regions. As the forests developed, bacterial and fungal communities' diversity changed, reached a minimum value at near-mature forests, and then increased in mature forests or over-mature forests. Near-mature forests had the lowest topological properties. The Shannon index of microbial communities varied with seasonal changes (P < 0.05). Bacterial and fungal community composition at genus level was more closely related to temperature indicators (including daily average temperature, daily maximum temperature, and daily minimum temperature) (P < 0.01, 0.5554 < R2 <0.8185) than daily average precipitation (P > 0.05, 0.0321 < R2 <0.6773). Bacteria were clustered by season and fungi were clustered by forest age. We suggested that extending the tree cultivation time of plantations could promote microbial community recovery. In addition, we found some species worthy of attention, including Bacteroidetes in autumn in over-mature forests, and Firmicutes in summer in young forests.IMPORTANCEChinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important fast-growing species with the largest artificial forest area in China, with the outstanding problems of low quality in soil. Soil microorganisms play a crucial role in soil fertility by decomposing organic matter, optimizing soil structure, and releasing essential nutrients for plant growth. In order to maintain healthy soil quality and prevent nutrient depletion and land degradation, it is crucial to understand the changes of soil microbial composition and diversity. Our study determined to reveal the change of soil microbial community from stand age, season, and the interaction between the two aspects, which is helpful to understand how interannual changes in different years and seasonal changes in one year affect soil fertility restoration and sustainable forest plantation management. It is a meaningful exploration of soil microbial communities and provides new information for further research.

Insights on the assembly processes and drivers of soil microbial communities in different depth layers in an abandoned polymetallic mining district

Soil microbes, which play crucial roles in maintaining soil functions and restoring degraded lands, are impacted by heavy metal pollution. This study investigated the vertical distribution of bacterial communities along the soil profiles across four types of areas (heavy metal pollution level: tailings heap area > phytoremediation area > natural restoration area > original forest area) in an abandoned polymetallic mining district by 16S rRNA sequencing, and aimed to disentangle the assembly mechanisms and key drivers of the vertical variation in bacterial community structure. Bacterial diversity and composition were found to vary remarkably between the depth layers in all types of areas, with heterogeneous selection dominated the vertical distribution pattern of soil bacterial communities. Pearson correlation analysis and partial Mantel test revealed that soil nutrients mainly shaped the vertical distribution of bacterial microbiota along soil profiles in the original forest and natural restoration areas. Ni, As, and bioavailable As were the key drivers regulating the vertical variation of bacterial assemblages in the phytoremediation area, whereas Pb, pH, soil organic carbon, and available nitrogen were crucial drivers in the tailings heap area. These findings reveal the predominant assembly mechanisms and drivers governing the vertical distribution of soil bacterial microbiota and indicate the efficiency of phytoremediation and ecological restoration on ameliorating edaphic micro-ecosystems in heavy metal-contaminated areas.

Improvement of phenolic acid autotoxicity in tea plantations by Pseudomonas fluorescens ZL22

Accumulation of phenolic acids, such as p-hydroxybenzoic acid (PHBA), 3,4 dihydroxybenzoic acid (PA), and cinnamic acid (CA) causes a decline in tea plantation soil quality. Bacterial strains that can balance phenolic acid autotoxicity (PAA) in tea tree rhizosphere soil are used to improve tea plantation soil. In this study, the effects of Pseudomonas fluorescens ZL22 on soil restoration and PAA regulation in tea plantations were investigated. ZL22 carries a complete pathway for degrading PHBA and PA to acetyl coenzyme A. ZL22 can colonise and reduce PHBA by 96% and PA by 98% in tea rhizosphere soil within 30 days. The cooccurrence of ZL22 and low CA levels further promotes lettuce seed growth and substantially increases tea production. ZL22 effectively regulates PAA to a safe level in rhizospheric soil, alleviating the inhibition of microbiota by PAA, increases the abundance of genera associated with soil N, C, and S cycling, and creates optimum pH (approximately 4.2) and organic carbon (approximately 25 g/kg), and available N (approximately 62 mg/kg) contents for secondary metabolite accumulation in tea leaves. The application of P. fluorescens ZL22 controls PAA, which synergistically improves plant growth and soil nutrition, thereby promoting tea production and quality.

The microbiome of buried soils demonstrates significant shifts in taxonomic structure and a general trend towards mineral horizons

Burial mounds represent a challenge for microbiologists. Could ancient buried soils preserve microbiomes as they do archaeological artifacts? To investigate this question, we studied the soil microbiome under a burial mound dating from 2500 years ago in Western Kazakhstan. Two soil profile cuts were established: one under the burial mound and another adjacent to the mound surface steppe soil. Both soils represented the same dark chestnut soil type and had the same horizontal stratification (A, B, C horizons) with slight alterations. DNA samples isolated from all horizons were studied with molecular techniques including qPCR and high throughput sequencing of amplicon libraries of the 16S rRNA gene fragment. The taxonomic structure of the microbiome of the buried horizons demonstrated a deep divergence from ones of the surface, comparable to the variation between different soil types (representatives of the soil types were included in the survey). The cause of this divergence could be attributed to diagenetic processes characterized by the reduction of organic matter content and changes in its structure. Corresponding trends in the microbiome structure are obvious from the beta-diversity pattern: the A and B horizons of the buried soils form one cluster with the C horizons of both buried and surface soil. This trend could generally be designated as 'mineralization'. Statistically significant changes between the buried and surface soils microbiomes were detected in the number of phylogenetic clusters, the biology of which is in the line of diagenesis. The trend of 'mineralization' was also supported by PICRUSt2 functional prediction, demonstrating a higher occurrence of the processes of degradation in the buried microbiome. Our results show a profound shift in the buried microbiome relatively the "surface" microbiome, indicating the deep difference between the original and buried microbiomes.

Expression, purification and crystallization of a novel metagenome-derived salicylaldehyde dehydrogenase from Alpine soil

Salicylaldehyde dehydrogenase (SALD) catalyses the last reaction in the upper pathway of naphthalene degradation: the oxidation of salicylaldehyde to salicylate. This enzyme has been isolated and studied from a few organisms that belong to the betaproteobacteria and gammaproteobacteria, predominantly Pseudomonas putida. Furthermore, there is only one crystal structure of this enzyme, which was obtained from P. putida G7. Here, crystallographic studies and analysis of the crystal structure of an Alpine soil metagenome-derived SALD (SALDAP) from an alphaproteobacterium are presented. The SALDAP gene was discovered using gene-targeted sequence assembly and it was cloned into a pLATE51 vector. The recombinant protein was overexpressed in Escherichia coli BL21 (DE3) cells and the soluble protein was purified to homogeneity. The protein crystallized at 20°C and diffraction data from the crystals were collected at a resolution of 1.9 Å. The crystal belonged to the orthorhombic space group C2221, with unit-cell parameters a = 116.8, b = 121.7, c = 318.0 Å. Analysis of the crystal structure revealed its conformation to be similar to the organization of the aldehyde dehydrogenase superfamily with three domains: the catalytic, NAD+-binding and bridging domains. The crystal structure of NahF from P. putida G7 was found to be the best structural homologue of SALDAP, even though the enzymes share only 48% amino-acid identity. Interestingly, a carboxylic acid (protocatechuic acid) was found to be a putative ligand of the enzyme and differential scanning fluorimetry was employed to confirm ligand binding. These findings open up the possibility of studying the mechanism(s) of product inhibition and biocatalysis of carboxylic acids using this enzyme and other related aldehyde dehydrogenases.

Trends in Microbial Community Composition and Function by Soil Depth

Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.

Nitrogen removal mechanism and microbial community changes of bioaugmentation subsurface wastewater infiltration system

Limited nitrogen removal capacity (mainly nitrate, NO₃^--N) remains a major challenge for subsurface wastewater infiltration system (SWIS). Two nitrogen-removing strains have been isolated from SWIS and inoculated to SWIS to investigate the effect of bioaugmentation on nitrogen removal performance and mechanism. The results showed bioaugmentation improved the removal efficiencies of NH₄⁺-N from 86.81% to 92.86% and TN from 74.90% to 86.55% and running stability compared to unbioaugmentation SWIS. 16 s rRNA amplicon sequencing results of the bacterial indicated that bioaugmentation altered the microbial community structure especially at 150 cm depth and increased the relative abundance of bacteria associated with nitrogen removal, significantly increasing the abundance of Rhizobiales_Incertae_Sedis and Lachnospiraceae. Furthermore, the relation between internal microbial characteristics and operational factors indicated that Hyphomicrobiaceae and Gemmatimonadaceae were also closely related to nitrogen removal. Predicted function profiles revealed that bioaugmentation enhanced the activity of nitrogen removal enzymes (Hao, NorBC, NasAB, NarGHI, NirBD and NosZ).

The distribution of novel bacterial laccases in alpine paleosols is directly related to soil stratigraphy

Bacterial laccases are now known to be abundant in soil and to function outside of the cell facilitating the bacterial degradation of lignin. In this study we wanted to test the hypotheses that: i) Such enzymes can be identified readily in stratified paleosols using metagenomics approaches, ii) The distribution of these genes as potential 'public good' proteins in soil is a function of the soil environment, iii) Such laccase genes can be readily retrieved and expressed in E. coli cloning systems to demonstrate that de novo assembly processes can be used to obtain similar metagenome-derived enzyme activities. To test these hypotheses, in silico gene-targeted assembly was employed to identify genes encoding novel type B two-domain bacterial laccases from alpine soil metagenomes sequenced on an Illumina MiSeq sequencer. The genes obtained from different strata were heterologously cloned, expressed and the gene products were shown to be active against two classical laccase substrates. The use of a metagenome-driven pipeline to obtain such active biocatalysts has demonstrated the potential for gene mining to be applied systematically for the discovery of such enzymes. These data ultimately further demonstrate the application of soil pedology methods to environmental enzyme discovery. As an interdisciplinary effort, we can now establish that paleosols can serve as a useful source of novel biocatalytic enzymes for various applications. We also, for the first time, link soil stratigraphy to enzyme profiling for widespread functional gene activity in paleosols.