Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Substratum-associated microbiota

© 2020 Water Environment Federation. Highlights of new, interesting, and emerging research findings on substratum-associated microbiota covered from a survey of 2019 literature from primarily freshwaters provide insight into research trends of interest to the Water Environment Federation and others interested in benthic, aquatic environments. Coverage of topics on bottom-associated or attached algae and cyanobacteria, though not comprehensive, includes new methods, taxa new-to-science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, and bloom-forming and harmful algae. Coverage of bacteria, also not comprehensive, focuses on the ecology of benthic biofilms and microbial communities, along with the ecology of microbes like Caulobacter crescentus, Rhodobacter, and other freshwater microbial species. Bacterial topics covered also include metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Readers may use this literature review to learn about or renew their interest in the recent advances and discoveries regarding substratum-associated microbiota. Practitioner points: This review of literature from 2019 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Coverage of algae and cyanobacteria includes findings on new methods, taxa new to science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, bloom-forming and harmful algae. Coverage of bacteria includes findings on ecology of benthic biofilms and microbial communities, the ecology of microbes, metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Highlights of new, noteworthy and emerging topics build on those from 2018 and will be of relevance to the Water Environment Federation and others interested in benthic, aquatic environments

New and interesting aerial diatom assemblages from southwestern Iceland

Examination of algal assemblages from aerial environments around the globe, especially those from pseudoaerial habitats found on moistened rocks underneath waterfalls or around springs and seeps, reveals the presence of unique diatom floras. Yet, diatom assemblages from northern regions like Iceland remain understudied, especially those from the volcanic rock outcrops and boulders that create euaerial habitats where biota receive moisture from the atmosphere or the rock itself. During the summers of 2013 and 2015, we examined the biodiversity of mostly euaerial, but also pseudoaerial, diatom assemblages collected from volcanic rock outcrops or large boulders on the landscape from southwestern Iceland. We used light and scanning electron microscopy to document the biodiversity of common, smaller, new, or interesting specimens, such as Humidophila and Eunotia. We describe one new Humidophila species, H. eldfjallii sp. nov., with triundulate valve margins and include information on another unidentified taxon, Humidophila sp. 1, naviculoid in shape with tapering to rounded ends, continuous striae through the length of the valve, and a circular central area. We formally transfer Diadesmis contenta var. biceps to Humidophila biceps. To correct the nomenclature, we recognized Humidophila parallela at the species level. Relative abundance estimates of diatom populations provided further characterization of the assemblages on these habitats. Humidophila taxa, especially H. gallica dominated the diverse diatom flora. We discuss adaptations for survival with access to mostly atmospheric water. The diatom flora described here adds to the flora for this region, highlights the diversity of diatom assemblages that can inhabit euaerial environments, and provides evidence of adaptive success of diatoms in extreme habitats with limited moisture and nutrients

New and interesting aerial diatom assemblages from southwestern Iceland

Examination of algal assemblages from aerial environments around the globe, especially those from pseudoaerial habitats found on moistened rocks underneath waterfalls or around springs and seeps, reveals the presence of unique diatom floras. Yet, diatom assemblages from northern regions like Iceland remain understudied, especially those from the volcanic rock outcrops and boulders that create euaerial habitats where biota receive moisture from the atmosphere or the rock itself. During the summers of 2013 and 2015, we examined the biodiversity of mostly euaerial, but also pseudoaerial, diatom assemblages collected from volcanic rock outcrops or large boulders on the landscape from southwestern Iceland. We used light and scanning electron microscopy to document the biodiversity of common, smaller, new, or interesting specimens, such as Humidophila and Eunotia. We describe one new Humidophila species, H. eldfjallii sp. nov., with triundulate valve margins and include information on another unidentified taxon, Humidophila sp. 1, naviculoid in shape with tapering to rounded ends, continuous striae through the length of the valve, and a circular central area. We formally transfer Diadesmis contenta var. biceps to Humidophila biceps. To correct the nomenclature, we recognized Humidophila parallela at the species level. Relative abundance estimates of diatom populations provided further characterization of the assemblages on these habitats. Humidophila taxa, especially H. gallica dominated the diverse diatom flora. We discuss adaptations for survival with access to mostly atmospheric water. The diatom flora described here adds to the flora for this region, highlights the diversity of diatom assemblages that can inhabit euaerial environments, and provides evidence of adaptive success of diatoms in extreme habitats with limited moisture and nutrients

Invertebrate grazing and epilithon assemblages control benthic nitrogen fixation in an N-limited river network

The effects of top-down (e.g., herbivory) and bottom-up (e.g., nutrient supply) processes on primary producers are often interdependent. In stream ecosystems, interactions between herbivorous grazers and physical factors, such as light and temperature, can alter the abundance and taxonomic composition of epilithic nitrogen (N) fixers. To examine how grazing and physical factors mediate the source ofNto stream ecosystems, we conducted an in-situ grazer exclusion experiment by removing crawling invertebrate grazers from epilithon-covered rocks in 3 streams with varying drainage areas, representing a gradient of temperature and light levels, within a northern California river network. After ∼1mo of grazer exclusion, we measured epilithon biomass and composition,N2 fixation, and ammonium (NH4), nitrate (NO3), and phosphate (PO4) uptake rates. Epilithic biomass, N2-fixation rates, and N and phosphorus uptake rates differed among the 3 streams, and rates were highest in the largest, open-canopy stream. Increases in N2-fixation rates with stream size were due to higher nitrogenase activity per unit of biomass as well as higher absolute biomass of N2 fixers. The presence of grazers interacted with physical factors to control nutrient fluxes. Ecologically-significant grazer removal effects only occurred in the largest stream, where grazing increased the influx of atmospheric N2 to the benthic biofilm. N2-fixation rates increased with grazing while NH4 uptake rates decreased by a similar proportion, shifting the predominant N source from the assimilation of dissolved N to atmospheric N2 via fixation by cyanobacteria. By altering the balance between N2 fixation and water column N uptake, grazers can mediate the flux of N to stream ecosystems

Taxon-specific photosynthetic responses of attached algal assemblages to experimental translocation between river habitats

Attached algal and cyanobacterial taxa differ in their ability to exploit and tolerate the diversity of flow, irradiance, and temperature regimes typical of a heterogeneous riverscape. Understanding the drivers of the small-scale variation in algal taxonomic composition helps us predict the riverscape-scale effects of altered flow regimes, but microhabitat-scale variation in algal taxonomy complicates the interpretation of ecosystem-scale estimates of bio-mass or primary production. Using pulse-amplitude modulated (PAM) fluorometry, we performed 2 manipulative field experiments (in 2014 and 2015) to measure photosynthetic responses of algae and cyanobacteria to depth, temperature, and flow modifications. In 2014, we exposed 6 attached algal assemblages common to the South Fork Eel River (California, USA) to a 24-h incubation on either the river bottom (20 cm deep) or floating at the water surface. In 2015, we incubated 3 algal assemblages for 1 wk in either the thalweg or at the river’s edge. For PAM measurements, we developed a novel method (Photosynthesis–Irradiance Periphyton Experimental System [PIPES]) for manipulating attached filamentous algae, a morphology common in aquatic habitats but underrepresented in photosynthesis experiments. To make the PIPES, we sandwiched thin (mm) layers of filamentous attached algae between 2 layers of mesh so that the algae could be isolated and manipulated for repeated PAM measurements. In the 2014 experiment, incubating Cladophora, Rivularia, Microcoleus, and Anabaena at the water surface tended to decrease photosynthetic rates relative to submerged controls, whereas for Nostoc, the photosynthetic rates were higher in floating treatments. In the 2015 experiment, Cladophora and Oedogonium incubated in the warmer, low-flow river margin had persistently lower photosynthesis rates than their counterparts incubated in the thalweg. The PIPES method improves our ability to make PAM measurements on attached algae. PIPES can be used in conjunction with other methods to evaluate taxon-specific responses to environmental conditions and to help us predict how algal assemblages will shift in dominance under different river management regimes

Substratum‐Associated Microbiota

Highlights of new, interesting, and emerging research findings on substratum‐associated microbiota covered from a survey of 2019 literature from primarily freshwaters, provide insight into research trends of interest to the Water Environment Federation and others interested in benthic, aquatic environments. Coverage of topics on bottom‐associated or attached algae and cyanobacteria, though not comprehensive, includes new methods, taxa new to science, nutrient dynamics, auto‐ and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, bloom‐forming and harmful algae. Coverage of bacteria, also not comprehensive, focuses on the ecology of benthic biofilms and microbial communities, along with the ecology of microbes like Caulobacter crescentus, Rhodobacter and other freshwater microbial species. Bacterial topics covered also include metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Readers may use this literature review to learn about or renew their interest in the recent advances and discoveries regarding substratum‐associated microbiota

Accurate whole human genome sequencing using reversible terminator chemistry

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications