Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation.

Background: Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

Cobalt-Catalyzed Regio-, Diastereo- and Enantioselective Reductive Coupling of 1,3-Dienes and Aldehydes.

Catalytic regio-, diastereo- and enantioselective reductive coupling of 1,3-dienes and aldehydes through regio- and enantioselective oxidative cyclization followed by regio- and diastereoselective protonation promoted by a chiral phosphine-cobalt complex is presented. Such processes represent an unprecedented reaction pathway for cobalt catalysis that enable selective transformation of the more substituted alkene in 1,3-dienes, affording a broad scope of bishomoallylic alcohols without the need of pre-formation of stoichiometric amounts of sensitive organometallic reagents in up to 98 % yield, >98 : 2 regioselectivity, >98 : 2 dr and 98 : 2 er. Application of this method to construction of axial stereogenicity and deuterated stereogenic center provided a wide range of multifunctional chiral building blocks that are otherwise difficult to access.

Inoculum source determines the stress resistance of electroactive functional taxa in biofilms: A metagenomic perspective.

The inoculum has a crucial impact on bioreactor initialization and performance. However, there is currently a lack of guidance on selecting appropriate inocula for applications in environmental biotechnology. In this study, we applied microbial electrolysis cells (MECs) as models to investigate the differences in the functional potential of electroactive microorganisms (EAMs) within anodic biofilms developed from four different inocula (natural or artificial), using shotgun metagenomic techniques.

Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics.

Background: Leakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes.

High speciation rate of niche specialists in hot springs.

Ecological and evolutionary processes simultaneously regulate microbial diversity, but the evolutionary processes and their driving forces remain largely unexplored. Here we investigated the ecological and evolutionary characteristics of microbiota in hot springs spanning a broad temperature range (54.8-80 °C) by sequencing the 16S rRNA genes.

Spatial distribution patterns across multiple microbial taxonomic groups.

Even in the vertical dimension, soil bacterial communities are spatially distributed in a distance-decay relationship (DDR). However, whether this pattern is universal among all soil microbial taxonomic groups, and how body size influences this distribution, remains elusive. Our study consisted of obtaining 140 soil samples from two adjacent ecosystems in the Yellow River Delta (YRD), both nontidal and tidal, and measuring the DDR between topsoil and subsoil for bacteria, archaea, fungi and protists (rhizaria).

The Stability of Phyto-Zooplanktonic Networks Varied with Zooplanktonic Sizes in Chinese Coastal Ecosystem.

The linkages between phytoplankton and zooplankton are crucial for the stability of complex food webs and the flow of energy within the marine ecosystem. Despite body size exhibiting multiple effects on the planktonic community assembly and the dispersal scale, its role in determining the stability of phyto-zooplanktonic co-occurrence patterns remains unclear. Here, we focused on more than 13,000 kilometers of the Chinese coast to study the diatom-dominated plankton ecosystem and to report the significant negative effects of zooplanktonic body sizes on the topological properties of phyto-zooplanktonic networks (PZNs) by using more than 500 species from 251 samples taken along the coastline.

ddPCR surpasses classical qPCR technology in quantitating bacteria and fungi in the environment.

Quantitative real-time PCR (qPCR) has been widely used in quantifying bacterial and fungal populations in various ecosystems, as well as the fungi to bacteria ratio (F:B ratio). Recently, researchers have begun to apply droplet digital PCR (ddPCR) to this area; however, no study has systematically compared qPCR and ddPCR for quantitating both bacteria and fungi in environmental samples at the same time. Here, we designed probe-primer pair combinations targeting the 16S rRNA gene and internal transcribed spacer (ITS) for the detection of bacteria and fungi, respectively, and tested both SYBR Green and TaqMan approaches in qPCR and ddPCR methods for mock communities and in real environmental samples.

iNAP: An integrated network analysis pipeline for microbiome studies.

Integrated network analysis pipeline (iNAP) is an online analysis pipeline for generating and analyzing comprehensive ecological networks in microbiome studies. It is implemented in two sections, that is, network construction and network analysis, and integrates many open-access tools. Network construction contains multiple feasible alternatives, including correlation-based approaches (Pearson's correlation and Spearman's rank correlation along with random matrix theory, and sparse correlations for compositional data) and conditional dependence-based methods (extended local similarity analysis and sparse inverse covariance estimation for ecological association inference), while network analysis provides topological structures at different levels and the potential effects of environmental factors on network structures.

Sampling cores and sequencing depths affected the measurement of microbial diversity in soil quadrats.

Due to the massive quantity and broad phylogeny, an accurate measurement of microbial diversity is highly challenging in soil ecosystems. Initially, the deviation caused by sampling should be adequately considered. Here, we attempted to uncover the effect of different sampling strategies on α diversity measurement of soil prokaryotes.

Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process.

Although many studies have investigated the spatial scaling of microbial communities living in surface soils, very little is known about the patterns within deeper strata, nor is the mechanism behind them. Here, we systematically assessed spatial scaling of prokaryotic biodiversity within three different strata (Upper: 0-20 cm, Middle: 20-40 cm, and Substratum: 40-100 cm) in a typical grassland by examining both distance-decay (DDRs) and species-area relationships (SARs), taxonomically and phylogenetically, as well as community assembly processes. Each layer exhibited significant biogeographic patterns in both DDR and SAR (p < .

Structural chromosome rearrangements and polymorphisms identified in Chinese wheat cultivars by high-resolution multiplex oligonucleotide FISH.

High-resolution multiplex oligonucleotide FISH revealed the frequent occurrence of structural chromosomal rearrangements and polymorphisms in widely grown wheat cultivars and their founders. Over 2000 wheat cultivars including 19 founders were released and grown in China from 1949 to 2000. To understand the impact of breeding selection on chromosome structural variations, high-resolution karyotypes of Chinese Spring (CS) and 373 Chinese cultivars were developed and compared by FISH (fluorescence in situ hybridization) using an oligonucleotide multiplex probe based on repeat sequences.

Development of oligonucleotides and multiplex probes for quick and accurate identification of wheat and Thinopyrum bessarabicum chromosomes.

In comparison with general FISH for preparing probes in terms of time and cost, synthesized oligonucleotide (oligo hereafter) probes for FISH have many advantages such as ease of design, synthesis, and labeling. Low cost and high sensitivity and resolution of oligo probes greatly simplify the FISH procedure as a simple, fast, and efficient method of chromosome identification. In this study, we developed new oligo and oligo multiplex probes to accurately and efficiently distinguish wheat (Triticum aestivum, 2n = 6x, AABBDD) and Thinopyrum bessarabicum (2n = 2x = 14, JJ) chromosomes.

Observations on the curative effect of lactulose for postpartum constipation based on a large sample study.

Unlabelled: To evaluate the efficacy and safety of lactulose in the intervention treatment of postpartum women with constipation.

Methods: The study adopted the multicenter clinical survey with a big sample which enrolled 4781 valid questionnaires from postpartum women in 18 different districts. All of them were treated with lactulose oral solution.