Ligation-dependent Cas14a1-Activated biosensor for one-pot pathogen diagnostic.

Pathogen identification requires nucleic acid diagnosis with simple equipment and fast manipulation. Our work established an all-in-one strategy assay with excellent sensitivity and high specificity, Transcription-Amplified Cas14a1-Activated Signal Biosensor (TACAS), for the fluorescence-based bacterial RNA detection. The DNA as a promoter probe and a reporter probe directly ligated via SplintR ligase once specifically hybridized to the single-stranded target RNA sequence, with the ligation product transcribed into Cas14a1 RNA activators by T7 RNA polymerase. This forming sustained isothermal one-pot ligation-transcription cascade produced RNA activators constantly and enabled Cas14a1/sgRNA complex to generate fluorescence signal, thus leading to a sensitive detection limit of 1.52 CFU mL-1E. coli within 2 h of incubation time. TACAS was applied in contrived E. coli infected fish and milk samples, and a significant signal differentiation between positive (infected) and negative (uninfected) samples was reached. Meanwhile, E. coli colonization and transmit time in vivo were explored and the TACAS assay promoted the understanding of the infection mechanisms of the E. coli infection, demonstrating an excellent detection capability.

Effects of wildfire disturbance on forest soil microbes and colonization of ericoid mycorrhizal fungi in northern China.

Wildfires affect forest succession and restoration by changing the community structure of soil microorganisms. Mycorrhizal formation is essential for plant growth and development. However, the driving mechanism of their natural succession after wildfire is still unclear. In this study, we examined the community structure of soil bacteria and fungi along a time series of natural recovery after wildfires in the Greater Khingan Range of China (2020 fires, 2017 fires, 2012 fires, 2004 fires, 1991 fires, and unburned). By exploring the effects of wildfire on plant traits, fruit nutrition, colonization of mycorrhizal fungi and its influencing mechanism. The results show that natural succession after wildfires significantly changed the community composition of bacteria and fungi, with ß diversity having a greater impact but less impact on the α diversity of microorganisms. Wildfires significantly changed plant traits and fruit nutrient content. The changes in colonization rate and customization intensity of mycorrhizal fungi were caused by increased MDA content and soluble sugar content and increased MADS-box gene and DREB1 gene expression in lingonberry (Vaccinium vitis-idaea L.). Our results showed that the soil bacterial and fungal communities in the boreal forest ecosystem changed significantly during wildfire recovery and changed the colonization rate of lingonberry mycorrhizal fungi. This study provides a theoretical basis for the restoration of forest ecosystems after wildfires.

Chromosome Three-Dimensional Structure Reconstruction: An Iterative ShRec3D Algorithm.

The three-dimensional (3D) structure of chromosomes is of great significance to ensure that the genome performs various functions (e.g., gene expression) correctly and replicates and separates correctly in mitosis. Since the emergence of Hi-C in 2009, a new experimental technique in molecular biology, researchers have been paying more and more attention to the reconstruction of chromosome 3D structure. To reconstruct the 3D structure of chromosomes based on Hi-C experimental data, many algorithms have been proposed, among which ShRec3D is one of the most outstanding. In this article, an iterative ShRec3D algorithm is presented to greatly improve the native ShRec3D algorithm. Experimental results show that our algorithm can significantly promote the performance of ShRec3D, and this improvement is applicable to almost all data noise range and signal coverage range, so it is universal.

Soil nutrients, forest structure and species traits drive aboveground carbon dynamics in an old-growth temperate forest.

Forests store a substantial amount of terrestrial carbon (C), but the drivers of forest C dynamics remain poorly understood, especially in old-growth forests. Here, we evaluate how aboveground C dynamics (i.e., net C change and its demographic processes: C gain from the growth of surviving trees (∆C-surv), C gain from the growth of recruited trees (∆C-recr) and C loss by tree mortality (∆C-mort)) are driven by vegetation attributes (diversity, trait composition and forest structure) and habitat conditions (soil properties and light environment), as well as how ∆C-surv, ∆C-recr and ∆C-mort contribute to net C change. Using 10-year interval demographic data from a 9-ha permanent plot in an old-growth temperate forest in northeastern China, we performed structural equation model to relate the C dynamics to the vegetation attributes and habitat conditions. The net C change is most strongly determined by ∆C-mort. High soil phosphorus concentrations increased ∆C-surv, soil moisture increased ∆C-recr, and leaf area index increased both ∆C-surv and ∆C-recr. Diversity (i.e., structural diversity) had a positive relationship with ∆C-surv but was not related to ∆C-recr or ∆C-mort. Trait composition was significantly related to all three demographic processes. Forest structure was the best predictor of ∆C-surv and ∆C-recr. The net C change increased with higher soil phosphorus concentrations and basal area and in communities dominated by conservative traits (i.e., high wood density). This study highlights that soil nutrients, forest structure and trait composition are important drivers of net C change in old-growth temperate forests. Better insights into C storage and productivity can be gained by simultaneously evaluating the vegetation attributes and habitat conditions of C dynamics in natural ecosystems.

Functional traits can improve our understanding of niche- and dispersal-based processes.

Ecologists often determine the relative importance of niche- and dispersal-based processes via variation partitioning based on species composition. Functional traits and their proxies of phylogeny are expected to increase the detection of niche-based processes and reduce the unexplained variation relative to species identity. We collected eight adult tree traits and phylogenetic data of 41 species and employed a phylogenetic fuzzy weighting method to address this issue in a 9-ha temperate forest dynamics plot. We used redundancy analysis to relate species, phylogenetic and functional compositions to environmental (soil resources and topography) and spatial variables. We also performed multi-scaled analyses on spatial variables by adding environment as the covariates to determine if functional traits increase the detection of niche-based processes at broad scales. The functional traits and intraspecific variation of the wood density among ontogenetic stages could dramatically increase the detection of niche-based processes and reduce the unexplained variation relative to species identity. Phylogenetic and functional compositions were mainly driven by total soil P and elevation, while species composition was weakly affected by multiple environmental variables. After controlling for the environment, a larger amount of the compositional variations in seed mass and maximum height were explained by finer-scaled spatial variables, indicating that dispersal processes may be important at fine spatial scales. Our results suggested that considering functional traits and their intraspecific variations could improve our understanding of ecological processes and increase our ability to predict the responses of plants to environmental change.

What factors potentially influence the ability of phylogenetic distance to predict trait dispersion in a temperate forest?

Although phylogenetic-based approaches have been frequently used to infer ecological processes, they have been increasingly criticized in recent years. To date, the factors that affect phylogenetic signals and further the ability of phylogenetic distance to predict trait dispersion have been assumed but not empirically tested. Therefore, we investigate which factors potentially influence the ability of phylogenetic distance to predict trait dispersion. We quantified the phylogenetic and trait dispersions across size classes and spatial scales in a 9-ha old-growth temperate forest dynamics plot in northeastern China. Phylogenetic signals at the community level were generally lower than those at the species pool level, and phylogenetically clustered communities showed lower phylogenetic signals than did overdispersed communities. This pattern might explain the other three findings of our study. First, phylogenetically overdispersed communities performed better at predicting trait dispersion than did clustered communities. Second, the mean pairwise distance (MPD)-based metric exhibited a stronger correlation with trait dispersion than did the mean nearest taxon distance (MNTD)-based metric. Finally, the MNTD-based metric showed that the prediction accuracy for trait dispersion decreased with increasing spatial scales, whereas its effects were weak on the MPD-based metric. In addition, phylogeny could not determine the dispersions of all functional axes but was able to predict certain traits depending on whether they were evolutionarily conserved. These results were conserved when we removed the effects of space and environment. Our findings highlighted that using phylogenetic distance as a proxy of trait similarity might work in a temperate forest depending on the species in local communities sampled from total pool as well as the traits measured. Utilizing these rules, we should rethink the conclusions of previous studies that were based on phylogenetic-based approaches.

Sample storage-induced changes in the quantity and quality of soil labile organic carbon.

Effects of sample storage methods on the quantity and quality of labile soil organic carbon are not fully understood even though their effects on basic soil properties have been extensively studied. We studied the effects of air-drying and frozen storage on cold and hot water soluble organic carbon (WSOC). Cold- and hot-WSOC in air-dried and frozen-stored soils were linearly correlated with those in fresh soils, indicating that storage proportionally altered the extractability of soil organic carbon. Air-drying but not frozen storage increased the concentrations of cold-WSOC and carbohydrate in cold-WSOC, while both increased polyphenol concentrations. In contrast, only polyphenol concentration in hot-WSOC was increased by air-drying and frozen storage, suggesting that hot-WSOC was less affected by sample storage. The biodegradability of cold- but not hot-WSOC was increased by air-drying, while both air-drying and frozen storage increased humification index and changed specific UV absorbance of both cold- and hot-WSOC, indicating shifts in the quality of soil WSOC. Our results suggest that storage methods affect the quantity and quality of WSOC but not comparisons between samples, frozen storage is better than air-drying if samples have to be stored, and storage should be avoided whenever possible when studying the quantity and quality of both cold- and hot-WSOC.

[Carbon density and production in valley spruce-fir forest in Xiaoxing'an Mountains, China].

The carbon density and production were measured using both forest inventory and allometry approaches in the declining valley spruce-fir forest in Xiaoxing' an Mountains. Results showed that the total carbon density of the forest was 268. 14 t C · hm(-2) in 2011, and carbon densities of the vegetation, detritus and soil were 74.25, 16.86 and 177.03 t C · hm(-2), respectively. From 2006 to 2011, tree layer carbon density decreased from 80.86 t C · hm(-2) to 71.73 t C · hm(-2). The average decrease proportions per year of carbon density were 0.5%, 1.2%, 2.7% and 3.7% for Abies nephrolepis, Betula platyphylla, Picea spp., and Larix gmelinii, respectively. However, carbon densities were increased by 2.9%, 3.9% and 7.2% per year for Alnus sibirica, Pinus koraiensis and Acer ukurunduense, respectively. Net primary production (NPP) of the forest was 4.69 t C · hm(-2) · a(-1). The ratio of belowground NPP to aboveground NPP was 0.56. Litterfall accounted for the largest proportion of the NPP of forest with a value of 34.5%. As the two most important carbon output approaches of forest ecosystems, the fluxes of heterotrophic respiration and coarse woody debris decomposition were 293.67 and 119.29 g C · m(-2) · a(-1), respectively. Net ecosystem production (NEP) of the forest was 55.90 g C · m(-2) a(-1). The results indicated that the valley spruce-fir forest in the declining state still had a certain carbon sink capacity.

[Effects of selective cutting on the carbon density and net primary productivity of a mixed broadleaved-Korean pine forest in Northeast China].

To accurately quantify forest carbon density and net primary productivity (NPP) is of great significance in estimating the role of forest ecosystems in global carbon cycle. By using the forest inventory and allometry approaches, this paper measured the carbon density and NPP of the virgin broadleaved-Korean pine (Pinus koraiensis) forest and of the broadleaved-Korean pine forest after 34 years selective-cutting (the cutting intensity was 30%, and the cutting trees were in large diameter class). The total carbon density of the virgin and selective-cutting broadleaved-Korean pine forests was (397.95 +/- 93.82) and (355.61 +/- 59.37) t C x hm(-2), respectively. In the virgin forest, the carbon density of the vegetation, debris, and soil accounted for 31.0%, 3.1%, and 65.9% of the total carbon pool, respectively; in the selective-cutting forest, the corresponding values were 31.7%, 2.9%, and 65.4%, respectively. No significant differences were observed in the total carbon density and the carbon density of each component between the two forests. The total NPP of the virgin and selective-cutting forests was (36.27 +/- 0.36) and (6.35 +/- 0.70) t C x hm(-2) x a(-1), among which, the NPP of overstory, understory, and fine roots in virgin forest and selective-cutting forest accounted for 60.3%, 2.0%, and 37.7%, and 66.1%, 2.0%, and 31.2%, respectively. No significant differences were observed in the total NPP and the contribution rate of each component between the two forests. However, the ratios of the needle and broadleaf NPPs of the virgin and selective-cutting forests were 47.24:52.76 and 20.48:79.52, respectively, with a significant difference. The results indicated that the carbon density and NPP of the broadleaved-Korean pine forest after 34 years selective-cutting recovered to the levels of the virgin broadleaved-Korean pine forest.