David M. Needham
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View article: Identifying and addressing the components of extreme physical-oceanographical events for improved risk management in coastal systems
Identifying and addressing the components of extreme physical-oceanographical events for improved risk management in coastal systems Open
Extreme physical-oceanographic events, such as marine heatwaves, fluvial floods, droughts and storm surges, have major impacts on local communities, economic sectors and ecosystems, and their frequency, intensity and duration increase due …
View article: The JEDI marker as a universal measure of planetary biodiversity
The JEDI marker as a universal measure of planetary biodiversity Open
Despite its critical importance in the formation and maintenance of ecosystems and homeostasis on Earth, biodiversity remains a complex and non-unified concept. Consequently, standards for measuring global biodiversity are lacking, hinderi…
View article: Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations
Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations Open
Viruses of microbes play important roles in ocean environments as agents of mortality and genetic transfer, influencing ecology, evolution and biogeochemistry. However, we know little about the diversity, seasonality, and host interactions…
View article: From Microscale to Microbial Insights: Validating High-Throughput Microvolume Extraction Methods (HiMEx) for Microbial Ecology
From Microscale to Microbial Insights: Validating High-Throughput Microvolume Extraction Methods (HiMEx) for Microbial Ecology Open
Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitate studying microbial communities where large-volume sample collection is challenging. This can aid w…
View article: Basin-scale dynamics and enrichment-enabled genomics of marine nitrifiers: seasonality, niches, interactions, and genomic uniqueness
Basin-scale dynamics and enrichment-enabled genomics of marine nitrifiers: seasonality, niches, interactions, and genomic uniqueness Open
Nitrification occurs widely from the deep sea to animal holobionts, but the eco-evolutionary forces shaping the niches and dynamics of the lineages of the chemoautotrophic bacteria and archaea responsible remain largely unknown. To make st…
View article: Greater host influence and promiscuity: how an invasive seaweed host has advantages over co-occurring natives
Greater host influence and promiscuity: how an invasive seaweed host has advantages over co-occurring natives Open
The surface microbiome of seaweed hosts is a multi-domain biofilm regulated by host-microbe and microbe-microbe interactions. The extent to which hosts influence these interactions, and potentially affect their resilience and invasion succ…
View article: From microscale to microbial insights: validating high-throughput microvolume extraction (HiMEx) methods for marine microbial ecology
From microscale to microbial insights: validating high-throughput microvolume extraction (HiMEx) methods for marine microbial ecology Open
Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitating the study of microbial communities where large-volume sample collection is challenging. This can…
View article: Multidisciplinary teaching cruise MNF-bioc-301 Plankton along the Baltic Sea salinity gradient, Cruise No. AL618, August 18th – August 30th 2024, Kiel (Germany) – Kiel (Germany), MNF-bioc-301
Multidisciplinary teaching cruise MNF-bioc-301 Plankton along the Baltic Sea salinity gradient, Cruise No. AL618, August 18th – August 30th 2024, Kiel (Germany) – Kiel (Germany), MNF-bioc-301 Open
The multidisciplinary teaching cruise AL618 was part of the curriculum of the master “Biological Oceanography” at the Christian-Albrechts-University Kiel and the GEOMAR Helmholtz Centre for Ocean Research. During this mandatory part of the…
View article: Greater host influence and promiscuity: How an invasive seaweed host has advantages over co-occurring natives
Greater host influence and promiscuity: How an invasive seaweed host has advantages over co-occurring natives Open
The surface microbiome of seaweed hosts is a multi-domain biofilm regulated by host-microbe and microbe-microbe interactions. The extent to which hosts influence these interactions, and potentially affect their resilience and invasion succ…
View article: Arctic Ocean virus communities: seasonality, bipolarity, and prokaryotic interactions
Arctic Ocean virus communities: seasonality, bipolarity, and prokaryotic interactions Open
Viruses play important roles in ocean environments as agents of mortality and genetic transfer, influencing ecology, evolution and biogeochemical processes. However, we know little about the diversity, seasonality, and host interactions of…
View article: Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions
Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions Open
Bacterial communities directly influence ecological processes in the ocean, and depth has a major influence due to the changeover in primary energy sources between the sunlit photic zone and dark ocean. Here, we examine the abundance and d…
View article: Ecological divergence of a mesocosm in an eastern boundary upwelling system assessed with multi-marker environmental DNA metabarcoding
Ecological divergence of a mesocosm in an eastern boundary upwelling system assessed with multi-marker environmental DNA metabarcoding Open
Eastern boundary upwelling systems (EBUS) contribute a disproportionate fraction of the global fish catch relative to their size and are especially susceptible to global environmental change. Here we present the evolution of communities ov…
View article: Comment on bg-2022-212
Comment on bg-2022-212 Open
Abstract. Eastern boundary upwelling systems (EBUS) contribute a disproportionate fraction of the global fish catch relative to their size and are especially susceptible to global environmental change. Here we present the evolution of comm…
View article: Ecological divergence of a mesocosm in an eastern boundary upwelling system assessed with multi-marker environmental DNA metabarcoding
Ecological divergence of a mesocosm in an eastern boundary upwelling system assessed with multi-marker environmental DNA metabarcoding Open
Eastern boundary upwelling systems (EBUS) contribute a disproportionate fraction of the global fish catch relative to their size and are especially susceptible to global environmental change. Here we present the evolution of communities ov…
View article: Genomes from Uncultivated Pelagiphages Reveal Multiple Phylogenetic Clades Exhibiting Extensive Auxiliary Metabolic Genes and Cross-Family Multigene Transfers
Genomes from Uncultivated Pelagiphages Reveal Multiple Phylogenetic Clades Exhibiting Extensive Auxiliary Metabolic Genes and Cross-Family Multigene Transfers Open
One of the most abundant and diverse marine bacterial groups is Pelagibacter . Phages have roles in shaping Pelagibacter ecology; however, several Pelagiphage lineages are represented by only a few genomes.
View article: The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate Open
Microbial predators such as choanoflagellates are key players in ocean food webs. Choanoflagellates, which are the closest unicellular relatives of animals, consume bacteria and also exhibit marked biological transitions triggered by bacte…
View article: A comparative study of flow cytometry‐sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant
A comparative study of flow cytometry‐sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant Open
Traditional or “bulk” viral enrichment and amplification methods used in viral metagenomics introduce unavoidable bias in viral diversity. This bias is due to shortcomings in existing viral enrichment methods and overshadowing by the more …
View article: High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome
High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome Open
Characterizing complex microbial communities with single-cell resolution has been a long-standing goal of microbiology. We present Microbe-seq, a high-throughput method that yields the genomes of individual microbes from complex microbial …
View article: ATP/ADP translocase alignment and phylogeny files
ATP/ADP translocase alignment and phylogeny files Open
#subtree file of ATP/ADP translocase alignment adpatp_alignment_subtree_mafft.sed.list.of.99bs.support.29jan2022.fa#subtree file of ATP/ADP translocase alignment, trimmedadpatp_trimmed_alignment_subtree_0.95.mafft.sed.list.of.99bs.support.…
View article: Virb4 secretion protein phylogeny full and subtree files
Virb4 secretion protein phylogeny full and subtree files Open
#virb4 trimmed alignment subtree, nexus formatvirb4_trimmed_alignment_nexus_subtree_comchoanosNotara.9Nov20.aln.masked.nex#virb4 trimmed alignment subtree, fasta formatvirb4_trimmed_alignment_subtree_comchoanosNoTara.9Nov20.aln.trimmed.fas…
View article: Rhodopsin phylogenetics with Comchoano
Rhodopsin phylogenetics with Comchoano Open
#rhodopsin alignment, fasta file untrimmedrhodopsin_alignment_mafft.w.gtdb.0.99.ordered.best.hits.and.ubas.and.changjae.fa.list.fa#rhodopsin alignment, fasta file trimmedrhodopsin_trimmed_alignment_trimal.mafft.w.gtdb.0.99.ordered.best.hit…
View article: 16S rRNA gene phylogeny files for Comchoano
16S rRNA gene phylogeny files for Comchoano Open
16S rRNA gene phylogeny of Comchoano, alignment and tripped files. Including raxml files and bayesian trees.#alignment file, full16S_alignment_mafft.cdhit.redo.w.genome.11000.1200.non.mito.representative.genome.list.fa.no.FPLS010.no.ambig.…
View article: Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts
Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts Open
The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), bu…
View article: Comprehensive <scp>single‐PCR 16S</scp> and <scp>18S rRNA</scp> community analysis validated with mock communities, and estimation of sequencing bias against <scp>18S</scp>
Comprehensive <span>single‐PCR 16S</span> and <span>18S rRNA</span> community analysis validated with mock communities, and estimation of sequencing bias against <span>18S</span> Open
Summary Universal primers for SSU rRNA genes allow profiling of natural communities by simultaneously amplifying templates from Bacteria, Archaea, and Eukaryota in a single PCR reaction. Despite the potential to show relative abundance for…
View article: <i>Microbe-seq</i>: high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome
<i>Microbe-seq</i>: high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome Open
We present Microbe-seq , a high-throughput single-microbe method that yields strain-resolved genomes from complex microbial communities. We encapsulate individual microbes into droplets with microfluidics and liberate their DNA, which we a…
View article: Seasonal and Geographical Transitions in Eukaryotic Phytoplankton Community Structure in the Atlantic and Pacific Oceans
Seasonal and Geographical Transitions in Eukaryotic Phytoplankton Community Structure in the Atlantic and Pacific Oceans Open
Much is known about how broad eukaryotic phytoplankton groups vary according to nutrient availability in marine ecosystems. However, genus- and species-level dynamics are generally unknown, although important given that adaptation and accl…
View article: Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities and denoising algorithms
Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities and denoising algorithms Open
Universal SSU rRNA primers allow comprehensive quantitative profiling of natural communities by simultaneously amplifying templates from Bacteria, Archaea, and Eukaryota in a single PCR reaction. Despite the potential to show all rRNA gene…