Environmental drivers of the resistome across the Baltic Sea.

Background: Antimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions.

PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.

Background: Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate.

Cross-taxa assessment of species diversity and phylogenetic structure of benthic communities in a dam-impacted river undergoing habitat restoration.

Exploring diversity and community composition patterns across evolutionary and functionally diverse organisms is critical for understanding the general processes that shape biodiversity in response to environmental changes. Knowledge of multi-trophic relationships offers valuable insights to support the effective assessment and management of freshwater ecosystems. In this study, we conducted a cross-taxa assessment of benthic macroinvertebrates and microorganisms using metabarcoding-based surveys to evaluate habitat restoration in a dam-impacted river.

Haplotype-level metabarcoding of freshwater macroinvertebrate species: A prospective tool for population genetic analysis.

Metabarcoding is a molecular-based tool capable of large quantity high-throughput species identification from bulk samples that is a faster and more cost-effective alternative to conventional DNA-sequencing approaches. Still, further exploration and assessment of the laboratory and bioinformatics strategies are required to unlock the potential of metabarcoding-based inference of haplotype information. In this study, we assessed the inference of freshwater macroinvertebrate haplotypes from metabarcoding data in a mock sample.

MetaLab-MAG: A Metaproteomic Data Analysis Platform for Genome-Level Characterization of Microbiomes from the Metagenome-Assembled Genomes Database.

The studies of microbial communities have drawn increased attention in various research fields such as agriculture, environment, and human health. Recently, metaproteomics has become a powerful tool to interpret the roles of the community members by investigating the expressed proteins of the microbes. However, analyzing the metaproteomic data sets at genome resolution is still challenging because of the lack of efficient bioinformatics tools.

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing.

Background: Sequential membrane filtration as a pre-processing step for capturing sediment-associated microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient temperatures before community profiling through culture-independent molecular techniques. However, the effects of sample pre-processing via filtration on DNA-based profiling of sediment-associated microbial community diversity and composition are poorly understood. Specifically, the influences of pre-processing on the quality and quantity of extracted DNA, high-throughput DNA sequencing reads, and detected microbial taxa need further evaluation.

Unraveling the Genetic Structure of the Coconut Scale Insect Pest ( Reyne) Outbreak Populations in the Philippines.

Despite the fact that massive outbreaks of the coconut scale insect pest, Reyne (Hemiptera: Diaspididae) are inflicting significant economic losses to the Philippines' coconut industry, little is known about the population and dispersal history of this invasive pest in the country. Here, we examined the genetic diversity, structure and demographic history of sampled from localities with reported outbreaks from 2014 to 2017. We analyzed the genetic structure of the outbreak populations using mitochondrial and nuclear markers.

Ecological influence of sediment bypass tunnels on macroinvertebrates in dam-fragmented rivers by DNA metabarcoding.

Sediment bypass tunnels (SBTs) are guiding structures used to reduce sediment accumulation in reservoirs during high flows by transporting sediments to downstream reaches during operation. Previous studies monitoring the ecological effects of SBT operations on downstream reaches suggest a positive influence of SBTs on riverbed sediment conditions and macroinvertebrate communities based on traditional morphology-based surveys. Morphology-based macroinvertebrate assessments are costly and time-consuming, and the large number of morphologically cryptic, small-sized and undescribed species usually results in coarse taxonomic identification.