Harry Witte - Academia.edu (original) (raw)

Papers by Harry Witte

Deposit-feeding holothurians often dominate the megafauna in bathyal deep-sea settings, in terms ... more Deposit-feeding holothurians often dominate the megafauna in bathyal deep-sea settings, in terms of both abundance and biomass. Molpadia musculus is particularly abundant at about 3400 m depth in the Nazaré Canyon on the NE Atlantic Continental Margin. However, these high abundances are unusual for burrowing species at this depth. The objective of this research was to understand the reasons of the massive occurrence of these molpadiid holothurians in the Nazaré Canyon. To address this question we investigated possible trophic interactions with bacteria at sites where the organic content of the sediment was different (Setú bal and Cascais Canyons, NE Atlantic Continental Margin). The molecular fingerprinting technique of Denaturing Gradient Gel Electrophoresis (DGGE) with band sequencing, combined with non-metric multidimensional scaling and statistical analyses, was used to compare the bacterial community diversity in canyon sediments and holothurian gut contents. Our results suggest that M. musculus does not need to develop a specialised gut bacterial community to aid digestion where the sediment is rich in organic matter (Nazaré Canyon); in contrast, such a community may be developed where the sediment is poorer in organic matter (Cascais Canyon).

Environmental Microbiology, Feb 1, 2017

An eight year time-series in the Western Antarctic Peninsula (WAP) with an approximately weekly s... more An eight year time-series in the Western Antarctic Peninsula (WAP) with an approximately weekly sampling frequency was used to elucidate changes in virioplankton abundance and their drivers in this climatically-sensitive region. Virioplankton abundances at the coastal WAP show a pronounced seasonal cycle with interannual variability in the timing and magnitude of the summer maxima. Bacterioplankton abundance is the most influential driving factor of the virioplankton, and exhibit closely coupled dynamics. Sea ice cover and duration predetermine levels of phytoplankton stock and thus, influence virioplankton by dictating the substrates available to the bacterioplankton. However, variations in the composition of the phytoplankton community and particularly the prominence of Diatoms inferred from silicate drawdown, drive inter-annual differences in the magnitude of the virioplankton bloom; likely again mediated through changes in the bacterioplankton. Our findings suggest that future warming within the WAP will cause changes in sea ice that will influence viruses and their microbial hosts through changes in the timing, magnitude and composition of the phytoplankton bloom. Thus the flow of matter and energy through the viral shunt may be decreased with consequences for the Antarctic food web and element cycling.

&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;p&amp;amp;amp;amp;amp;amp;amp;amp;amp... more &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;Ocean plastic debris poses a large threat to the marine environment. Millions of tons of plastic end up in the ocean each year and the Mediterranean Sea is one of the most plastic polluted sea. Ocean plastic particles are typically covered with microbial biofilms, but it remains unclear if different polymer types are colonized by different communities. Knowledge in this aspect strengthens our understanding if microbes purely use plastic debris as attachment surface or if they may even contribute to the degradation of plastic. To gain a better understanding of the composition and structure of biofilms on micro plastic particles (MP) in the Mediterranean Sea, we analyzed microbial community covering floating MP in a bay/marina (Marina di Campo) on the island of Elba. MPs were collected with a plankton net (mesh size 50&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#181;m), fixed for fluorescence microscopy and stored for subsequent DNA extraction, and identification of the polymer with Raman spectroscopy. The particles were mainly comprised of polyethylene (PE), polypropylene (PP) and polystyrene (PS) and were often brittle and with cracks (PE, PP) and showed visual signs of biofouling (PE, PP, PS). Fluorescence in situ hybridization and imaging by high resolution confocal laser scanning microscopy of single MPs revealed high densities of colonization by microbes. 16S rRNA gene amplicon sequencing (Illumina Miseq) revealed higher abundance of archaeal sequences on PS (up to 29% of the reads) in comparison to PE or PP (up to 3% of the reads). &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#160;The bacterial community in the biofilms on each of the three plastic types consisted mainly of the orders Flavobacteriales, Rickettsiales, Alteromonadales, Cytophagales, Rhodobacterales and Oceanospirillales. Furthermore, we found significant difference in the community composition of biofilms on PE compared to PP and PS but not between PP and PS. The indicator species on PE were Calditrichales, detected at 10 times higher sequence abundance on PE than on PP and PS, as well as several uncultured orders. This study sheds light on preferential microbial attachment and biofilm formation on microplastic particles, yet it remains to be revealed, whether and which of these may contribute to plastic degradation.&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;

ABSTRACTMarker gene sequencing of the rRNA operon (16S, 18S, ITS) or cytochrome c oxidase I (CO1)... more ABSTRACTMarker gene sequencing of the rRNA operon (16S, 18S, ITS) or cytochrome c oxidase I (CO1) is a popular means to assess microbial communities of the environment, microbiomes associated with plants and animals, as well as communities of multicellular organisms via environmental DNA sequencing. Since this technique is based on sequencing a single gene rather than the entire genome, the number of reads needed per sample is lower than that required for metagenome sequencing, making marker gene sequencing affordable to nearly any laboratory. Despite the relative ease and cost-efficiency of data generation, analyzing the resulting sequence data requires computational skills that may go beyond the standard repertoire of a current molecular biologist/ecologist. We have developed Cascabel, a flexible and easy-to-use amplicon sequence data analysis pipeline, which uses Snakemake and a combination of existing and newly developed solutions for its computational steps. Cascabel takes the ...

Journal of Phycology

The Dutch coastal zone is a region of the North Sea with a marked interannual and long‐term abiot... more The Dutch coastal zone is a region of the North Sea with a marked interannual and long‐term abiotic and phytoplankton variability. To investigate the relationship between abiotic variability and phytoplankton composition, two routine water monitoring data sets (1991–2005) were examined. Multivariate statistics revealed two significant partitions in the data. The first consisted of interannual abiotic fluctuations that were correlated to Rhine discharge that affected the abundance of summer and autumn diatom species. The second partition was caused by a shift in the abiotic data from 1998 to 1999 that was followed by a shift in phytoplankton composition from 1999 to 2000. Important factors in the abiotic shift were decreases in suspended matter (SPM) and phosphate (DIP) concentrations, as well as in pH. The decrease in SPM was caused by a reduction in wind speed. The increase in water column daily irradiance from the decrease in SPM led to increases in the abundance of winter–spring species, notably the prymnesiophyte Phaeocystis globosa. Because wind speed is related to the North Atlantic Oscillation (NAO) index it was possible to correlate NAO index and P. globosa abundance. Only five abiotic variables representing interannual and long‐term variability, including Rhine discharge and NAO index, were needed to model the observed partitions in phytoplankton composition. It was concluded that interannual variability in the coastal phytoplankton composition was related to year‐to‐year changes in river discharge while the long‐term shift was caused by an alternating large‐scale meteorological phenomenon.

The effect of iron on phytoplankton physiology in a scarcely investigated part of the Pacific reg... more The effect of iron on phytoplankton physiology in a scarcely investigated part of the Pacific region of the Southern Ocean was studied during an expedition aboard RV 'Polarstern' Physiological effects of iron enrichments were studied during short-term bottle experiments (72 h) in highnutrient, low-chlorophyll (HNLC) water samples. Throughout the expedition (March to May 1995), surface water nitrate concentrations were high (21 to 27 pM) and surface water silicate concentrations varied considerably north (<3.5 pM) and south (> l 3 pM) of the Polar Front, whereas low chlorophyll a concentrations (<0.2 pg I-') were measured in the research area. Small-sized cells (<S pm) dominated the phytopianicton communiiy; & d i~l l l b w e l e observed only occasionci!:Y north G! thc Po!ar Prent. Tcta! phytoplankton numbers, as determined by flow cytometry, ranged from 1500 to 8000 cells ml-l. Ambient dissolved iron concentrations in the experimental area were low and ranged from 0.1 to 0.4 nM in surface waters. In the experimental series, indications of iron stress in the indigenous phytoplankton assemblage were found. Whereas the species composition remained virtually unaltered upon addition of 2 nM iron, significant increases in nitrate uptake and enhanced nitrate reductase activities were observed withln 32 h after the start of the experin~ents. Ammonium uptake, which prevailed over nitrate uptake, remained unaltered by the iron additions. In addition to the physiological effects, a molecular marker of lron stress, flavodoxin, was detected in phytoplankton protein extracts collected after 72 h of incubation. Irrespective of iron deficiency, silicate concentrations in the northern part of the research area were llkely below half-saturation values for growth for hatoms and thereby likely prevented diatom blooms. The results of this study indicate that the nano-phytoplankton in the Pacific region of the Southern Ocean are iron stressed; upon iron enrichment, a physiological stimulation is observed. Our results support a lack of iron as one of the causes of HNLC conditions in this region.

Environmental DNA

This is an open access article under the terms of the Creative Commons Attribution License, which... more This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Fems Microbiol Ecol, 2002

Uni-algal, non-axenic cultures of six marine diatoms were screened by polymerase chain reaction^d... more Uni-algal, non-axenic cultures of six marine diatoms were screened by polymerase chain reaction^denaturing gradient gel electrophoresis for the diversity of the accompanying bacterial communities ('satellite' bacteria) in order to test the hypothesis that algal cells constitute niches for specific bacterial species. The complexity of the satellite assemblages, as judged from the number of detected phylotypes, was low when compared to the complexity of bacterial assemblages in nature. Generally, the six algal cultures were accompanied by distinct satellite assemblages, as the majority of the phylotypes detected in the six cultures were unique, and only some phylotypes were common to more than one culture. Analysis of replicate incubations and repeated passage of cultures in most cases showed only minor variations in satellite assemblage genetic fingerprints, suggesting that the bacterial^algal associations were stable. An experimental approach to find evidence for specific bacterial^algal interactions by challenging algal cultures with heterologous satellite assemblages was unsuccessful as it was not possible to avoid carryover of algae. Satellite populations were identified by sequencing of denaturing gradient gel electrophoresis bands. Most of the populations represented typical marine phylotypes, such as members of the K-Proteobacteria (related to the genera Ruegeria, Sulfitobacter, Roseobacter and Erythrobacter), or members of different genera of the Cytophaga-Flavobacterium-Bacteroides (CFB) phylum. Surprisingly, L-Proteobacteria were also found in two of the cultures. A common point for all cultures was the presence of at least one representative of the K-Proteobacteria and of the CFB phylum, both of which have been reported as important representatives of the marine picoplankton. Their ubiquity in the sea and in the phytoplankton cultures analysed points to a specific role of these bacteria in the marine food web. The results indicate that algal diversity might be an important factor in explaining the enormous bacterial diversity in marine assemblages, and vice versa. Specific substances in the photosynthetic extracellular release and in the organic carbon produced by different phytoplankton species may require a variety of bacterial populations for the processing of this algal-derived organic matter. ß

We analysed the diversity and abundance of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in ... more We analysed the diversity and abundance of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in the shallow warm-water sponge Halisarca caerulea and the deep cold-water sponges Higginsia thielei and Nodastrella nodastrella. The abundance of AOA and AOB was analysed using catalyzed reporter deposition-fluorescence in situ hybridization and (real-time) quantitative PCR (Q-PCR) targeting archaeal and bacterial amoA genes. Archaeal abundance was similar between sponge species, while bacterial abundance was higher in H. caerulea than in N. nodastrella and H. thielei. Q-PCR showed that AOA outnumbered AOB by a factor of 2 to 35, suggesting a larger role of AOA than of AOB in ammonia oxidation in sponges. PCR-denaturing gradient gel electrophoresis was performed to analyse the taxonomic affiliation of the microbial community associated with these sponges. Archaeal and bacterial amoA genes were found in all 3 sponges. The structure of the phylogenetic trees in relation to temperature and sponge species was analysed using all published amoA sequences retrieved from sponges. Temperature was an important factor influencing the distribution of nitrifiers in sponges. Both archaeal and bacterial amoA sponge sequences tended to cluster with sequences retrieved from habitats of similar temperature. This is the first time that similarity in AOB diversity is described between distantly related species (H. thielei belonging to the class Demospongiae, and N. nodastrella to Hexactinellida). The results described here support the idea of a relatively uniform microbial community between distantly related sponges and suggest that temperature (rather than phylogenetic distance) is determining the diversity of AOA and AOB in sponges.

... SPRING OUTBURST OF PLEUROBRACHIA PILEUS BOUWE R. KUIPERS, URSULA GAEDKE,LISETTE ENSERINK and ... more ... SPRING OUTBURST OF PLEUROBRACHIA PILEUS BOUWE R. KUIPERS, URSULA GAEDKE,LISETTE ENSERINK and ... Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The ... outbursts of Pleurobrachia pileus that some-times occur in spring (VAN DER BAAN ...

Biogeosciences Discussions, 2015

This study characterizes the microbial community composition over Haas Mound, one of the most pro... more This study characterizes the microbial community composition over Haas Mound, one of the most prominent cold-water coral mounds of the Logachev Mound province (Rockall Bank, NE Atlantic). We outline patterns of distribution vertically -from the seafloor to the water column -and laterally -across the mound -and couple these to mound topography and hydrography. Samples of water, sediment and Lophelia pertusa were collected in 2012 and 2013 from locations that were chosen based on high definition video surveys. Temperature and current measurements were obtained at two sites at the summit and foot of Haas Mound to study near-bed hydrodynamic conditions. Overlaying water was collected from depths of 400 m as well as 5 and 10 m above the bottom using a CTD/Rosette system. Near-bottom water, sediment and L. pertusa mucus and skeleton samples were obtained with a box corer. Of all these biotopes, Roche GS-FLX amplicon sequencing targeting both Bacteria and Archaea was carried out, augmenting our understanding of deep sea microbial consortia. The pattern of similarities between samples, visualized by multi-dimensional scaling (MDS), indicates a strong link between the distribution of microbes and the specific biotopes. The microbial operational taxonomic unit (OTU) diversity was the highest in near-bottom water, which was sampled in the coral framework. For the first time, Thaumarchaeota marine group I (MGI) were found in L. pertusa mucus; Endozoicomonas was detected in skeleton, mucus and near-bottom water, whereas Mycoplasma was only detected in skeleton and near-bottom water, however not in mucus. Analysis of similarities (ANOSIM) indicates that overlaying water is well-mixed at 400 m depth but less so at 5 and 10 m above the bottom, where the composition of microbial communities differed significantly between summit, slope and off-mound. At all locations, the near-bottom water differed significantly from water at 5 m above the bottom, illustrating that the near-bottom water in between the coral framework represents a separate microbial habitat. Furthermore, the observed spatial heterogeneity in microbial communities is discussed in relation to environmental conditions.

Limnology and Oceanography, 2012

ABSTRACT

Marine Ecology Progress Series, 1998

Effects of iron stress on chromatic adaptation were studied in natural phytoplankton communities ... more Effects of iron stress on chromatic adaptation were studied in natural phytoplankton communities collected in the Pacific region of the Southern Ocean. Iron enrichment experiments (48 to 72 h) were performed, incubating plankton comn~unities under white, green and blue light respectively, with and without addition of 2 nM Fe. Pigment ratios were affected by iron addition only to a minor extent. The pigment composition as dictated by the light conditions was similar for both the ironenriched and the unamended bottles. Upon iron addition, phytoplankton auto-fluorescence, as estimated by flow cytometry, decreased markedly, indicating iron stress of the endemic phytoplankton community. It was concluded that iron did not control chromatic adaptation via the pigment composition, but exerted a clear effect on the efficiency of electron transfer KEY MJORDS: Iron .

Marine Ecology Progress Series, 2000

Growth rates in prochlorophytes and their loss rates to grazing were investigated by the dilution... more Growth rates in prochlorophytes and their loss rates to grazing were investigated by the dilution technique in the lower euphotic zone of the (sub)tropical North Atlantic. Directly above the 'deep chlorophyll maximum' (DCM), prochlorophyte growth rates were approximately 0.3 d -1 and grazing rates 0.4 d -1 ; both rates were considerably lower in and directly below the DCM. Grazing was only weakly affected by filtration through 3 µm pore-size filters, indicating heterotrophic nanoflagellates as the main grazers. Discrimination between day and night revealed that the prochlorophytes above the DCM, with doubling times of 3 d or more, divided during the day whereas at greater depth division occurred during the night. In contrast, grazing was always restricted to the daylight period and grazing rate was independent of prochlorophyte abundance, growth rate or time of division. Prochlorophyte grazing rates were, however, correlated with the loss rates in the much more abundant heterotrophic bacteria in the same layers. We conclude therefore that prochlorophytes are consumed as a secondary prey by heterotrophic nanoflagellates grazing on heterotrophic bacteria.

Marine Ecology Progress Series, 1999

The impact of microzooplankton community grazing on different size classes of algae was investiga... more The impact of microzooplankton community grazing on different size classes of algae was investigated at 11 stations between Dogger Bank and the Shetlands in early spring (March-April) and in summer (July-August). Thls work is part of a larger study designed to test the hypothesis that sizedifferential grazing of phytoplankton populations plays a crucial role in regulating food web structure. Dilution experiments, in which loss rates of the algae due to microzooplankton grazing can be estimated from the relation between growth rate of the prey and dilution, failed in many cases due to high variance. The present paper analyses the problem and puts forward a solution which involved pooling data from comparable stations into 1 average grazing estimate per algal size class. In early spring, estimates of grazing from measurements of chlorophyll a (chl a) were obta.ined only for algae > 5 pm, and average grazing rate was 0.23 d-l at the deeper stations. At the shallower more southern stations where a phytoplankton bloom was in progress the average grazing rate on algae >5 pm was 0.5 d-' Flow cytometry was more successful in the < 5 pm algal fraction, yielding grazing rates of 0.25 d-' for the southern and 0 31 d-l for the northern stations. In summer, microzooplankton grazing incubations y~elded significant results only when flow cytometry was used, and only when results were pooled for different areas. Grazing rates ranged from 0.07 d-' in the 1-2 pm algal size class to 0.74 d-' for algae of 3-4 pm and were 0.25 d-' for the <5 pm cluster as a whole.