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Article ; Online: Recovery patterns of the coral microbiome after relief of algal contact

Duyl, Fleur C. van / van Bleijswijk, Judith D.L. / Wuchter, Cornelia / Witte, Harry J. / Coolen, Marco J.L. / Bak, Rolf P.M. / Engelmann, Julia C. / Nugues, Maggy M.

Journal of Sea Research. 2023 Feb., v. 191 p.102309-

2023

Abstract: Interactions between macroalgae and corals are omnipresent on eutrophied and overfished reefs worldwide. Contact with macroalgae can disrupt corals and their microbiomes through diverse mechanisms, including shading, abrasion, and the release of algal ... ...

Abstract	Interactions between macroalgae and corals are omnipresent on eutrophied and overfished reefs worldwide. Contact with macroalgae can disrupt corals and their microbiomes through diverse mechanisms, including shading, abrasion, and the release of algal exudates. However, changes in the coral microbiome after algal contact ceases have not been studied. We investigated the recovery of the microbiome of massive reef-building Porites corals following experimental removal of the overgrowing green macroalga Halimeda macrophysa. We followed changes in the microbiome of macroalgal-removed and adjacent healthy-looking tissue of coral colonies over 40 days. Coral tissue was predominantly bleached underneath the macroalgae but regained almost its full pigmentation by day 40. Despite this recovery in pigmentation, the bacterial microbiome of macroalgal-removed coral tissue did not return to that of adjacent healthy-looking tissue (control). Overall, macroalgal contact led to the suppression of Gammaproteobacteria and increased diversity and dominance of Alphaproteobacteria, a shift that persevered for 40 days after algal removal. Causal effect analysis showed a positive effect of influential OTUs in healthy-looking tissue assigned to Gammaproteobacteria and Bacteroidia on the relative abundance of other OTUs within these classes. The effect of influential OTUs assigned to Alphaproteobacteria in macroalgal-removed tissue on the relative abundance of other OTUs was more diverse. Despite the high heterogeneity of coral microbiomes, differences in the relative abundance of main bacterial classes and orders between control/healthy and macroalgal-removed tissue showed temporal patterns. Differences in the Alpha-, Gamma-, Deltaproteobacteria and Bacteroidia between control/healthy and macroalgal-removed tissue increased after cessation of macroalga contact and stabilized or declined towards day 40. Acidimicrobiia, Deltaproteobacteria, Rhodospirillales and Rhodovibrionales returned to average relative abundances in the adjacent control/healthy tissue after 40 days. Nevertheless, Rhizobiales and Rhodobacterales (Alphaproteobacteria) still dominated the macroalgal-removed microbiome on day 40. We conclude that macroalgal overgrowth induces changes in the coral microbiome, and that algal removal did not lead to full recovery of the microbiome in 40 days. Return of pigmentation and distinct shifts in bacterial groups over time appear a possible pathway to the recovery of the coral microbiome after macroalgal removal.
Keywords	Bacteroidia ; Halimeda ; Rhizobiales ; Rhodobacterales ; Rhodospirillales ; corals ; delta-Proteobacteria ; gamma-Proteobacteria ; macroalgae ; microbiome ; overfishing ; pigmentation ; research ; Coral-algal interaction ; Coral microbiome dynamics ; Recovery
Language	English
Dates of publication	2023-02
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Use and reproduction
ISSN	1385-1101
DOI	10.1016/j.seares.2022.102309
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: Bacteriohopanetetrol-x

Kemenade, Zoë R. / Villanueva, Laura / Hopmans, Ellen C. / Kraal, Peter / Witte, Harry J. / Sinninghe Damsté, Jaap S. / Rush, Darci

eISSN: 1726-4189

constraining its application as a lipid biomarker for marine anammox using the water column oxygen gradient of the Benguela upwelling system

2022

Abstract: Interpreting lipid biomarkers in the sediment archive requires a good understanding of their application and limitations in modern systems. Recently it was discovered that marine bacteria performing anaerobic ammonium oxidation (anammox), belonging to ... ...

Abstract	Interpreting lipid biomarkers in the sediment archive requires a good understanding of their application and limitations in modern systems. Recently it was discovered that marine bacteria performing anaerobic ammonium oxidation (anammox), belonging to the genus Ca. Scalindua, uniquely synthesize a stereoisomer of bacteriohopanetetrol (“BHT- x ”). The ratio of BHT- x over total bacteriohopanetetrol (BHT, ubiquitously synthesized by diverse bacteria) has been suggested as a proxy for water column anoxia. As BHT has been found in sediments over 50 Myr old, BHT- x has the potential to complement and extend the sedimentary biomarker record of marine anammox, conventionally constructed using ladderane lipids. Yet, little is known about the distribution of BHT- x in relation to the distribution of ladderanes and to the genetic evidence of Ca. Scalindua in modern marine systems. Here, we investigate the distribution of BHT- x and the application of the BHT- x ratio in relation to distributions of ladderane intact polar lipids (IPLs), ladderane fatty acids (FAs) and Ca. Scalindua 16S rRNA genes in suspended particulate matter (SPM) from the water column of the Benguela upwelling system (BUS), sampled across a large oxygen gradient. In BUS SPM, high BHT- x abundances were restricted to the oxygen-deficient zone on the continental shelf (at [O 2 ] < 45 µ mol L −1 , in all but one case). High BHT- x abundances co-occurred with high abundances of the Ca. Scalindua 16S rRNA gene (relative to the total number of bacterial 16S rRNA genes) and ladderane IPLs. At shelf stations with [O 2 ] > 50 µ mol L −1 , the BHT- x ratio was < 0.04 (in all but one case). In apparent contradiction, ladderane FAs and low abundances of BHT and BHT- x (resulting in BHT- x ratios > 0.04) were also detected in oxygenated offshore waters ([O 2 ] up to 180 µ mol L −1 ), whereas ladderane IPLs were undetected. The index of ladderane lipids with five cyclobutane rings (NL 5 ) correlates with in situ temperature. NL 5 -derived temperatures suggested that ladderane FAs in the offshore waters were not synthesized in situ but were transported down-slope from warmer shelf waters. Thus, in sedimentary archives of systems with known lateral organic matter transport, such as the BUS, relative BHT and BHT- x abundances should be carefully considered. In such systems, a higher BHT- x ratio may act as a safer threshold for deoxygenation and/or Ca. Scalindua presence: our results and previous studies indicate that a BHT- x ratio of ≥ 0.2 is a robust threshold for oxygen-depleted waters ([O 2 ] < 50 µ mol kg −1 ). In our data, ratios of ≥ 0.2 coincided with Ca. Scalindua 16S rRNA genes in all samples ( n =62 ), except one. Lastly, when investigating in situ anammox, we highlight the importance of using ladderane IPLs over BHT- x and/or ladderane FAs; these latter compounds are more recalcitrant and may derive from transported fossil anammox bacteria remnants.
Subject code	511 ; 333
Language	English
Publishing date	2022-01-13
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Cascabel

Abdala Asbun, Alejandro / Besseling, Marc A / Balzano, Sergio / van Bleijswijk, Judith D L / Witte, Harry J / Villanueva, Laura / Engelmann, Julia C

Frontiers in genetics

2020 Volume 11, Page(s) 489357

Abstract: Marker 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 ... ...

Abstract	Marker 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
Language	English
Publishing date	2020-11-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2020.489357
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Article: Microbial Communities on Plastic Polymers in the Mediterranean Sea.

Vaksmaa, Annika / Knittel, Katrin / Abdala Asbun, Alejandro / Goudriaan, Maaike / Ellrott, Andreas / Witte, Harry J / Vollmer, Ina / Meirer, Florian / Lott, Christian / Weber, Miriam / Engelmann, Julia C / Niemann, Helge

Frontiers in microbiology

2021 Volume 12, Page(s) 673553

Abstract: Plastic particles in the ocean are typically covered with microbial biofilms, but it remains unclear whether distinct microbial communities colonize different polymer types. In this study, we analyzed microbial communities forming biofilms on floating ... ...

Abstract	Plastic particles in the ocean are typically covered with microbial biofilms, but it remains unclear whether distinct microbial communities colonize different polymer types. In this study, we analyzed microbial communities forming biofilms on floating microplastics in a bay of the island of Elba in the Mediterranean Sea. Raman spectroscopy revealed that the plastic particles mainly comprised polyethylene (PE), polypropylene (PP), and polystyrene (PS) of which polyethylene and polypropylene particles were typically brittle and featured cracks. Fluorescence
Language	English
Publishing date	2021-06-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2021.673553
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Bacteriohopanetetrol-x

Kemenade, Zoë Rebecca / Villanueva, Laura / Hopmans, Ellen C. / Kraal, Peter / Witte, Harry J. / Sinninghe Damsté, Jaap S. / Rush, Darci

eISSN: 1726-4189

constraining its application as a lipid biomarker for marine anammox using the water column oxygen gradient of the Benguela upwelling system

2021

Abstract	Interpreting lipid biomarkers in the sediment archive requires a good understanding of their application and limitations in modern systems. Recently it was discovered that marine bacteria performing anaerobic ammonium oxidation (anammox), belonging to the genus Ca . Scalindua, uniquely synthesize a stereoisomer of bacteriohopanetetrol (‘BHT- x ’). The ratio of BHT- x over total bacteriohopanetetrol (BHT; ubiquitously synthesized by diverse bacteria) has been suggested as a proxy for water column anoxia. As BHT has been found in sediments over 50 Myr old, BHT- x has the potential to complement and extend the sedimentary biomarker record of marine anammox, conventionally constructed using ladderane lipids. Yet, little is known about the distribution of BHT- x in relation to the distribution of ladderanes and to the genetic evidence of Ca . Scalindua in modern marine systems. Here, we investigate the distribution of BHT- x and the application of the BHT- x ratio in relation to distributions of intact polar (IPL) ladderane lipids, ladderane fatty acids (FAs) and Ca . Scalindua 16S rRNA genes in suspended particulate matter (SPM) from the water column, sampled across a large oxygen gradient in the Benguela upwelling system (BUS). In BUS SPM, high BHT- x abundances were constrained to the oxygen deficient zone on the continental shelf (at [O 2 ] < 45 µmol L −1 , in all but one case). High BHT- x abundances co-occurred with high abundances of the Ca . Scalindua 16S rRNA gene (relative to the total number of bacterial 16S rRNA genes) and ladderane IPLs. At shelf stations with [O 2 ] > 50 µmol L −1 , the BHT- x ratio was < 0.04 (in all but one case). In apparent contradiction, ladderane FAs and low abundances of BHT and BHT- x (resulting in BHT- x ratio’s > 0.04) were also detected in oxygenated offshore waters ([O 2 ] up to 180 µmol L −1 ), whereas ladderane IPLs were undetected. NL5-derived temperatures suggested that ladderane FAs in the offshore waters were not synthesized in situ but derived from warmer shelf waters. Thus, in sedimentary archives of systems with known lateral organic matter transport, such as the BUS, relative BHT and BHT- x abundances should be carefully considered. In such systems, a higher BHT- x ratio may act as a safer threshold for deoxygenation and/or Ca . Scalindua presence: in the BUS, at [O 2 ] > 50 µmol L −1 , the BHT- x ratio was < 0.18 at both off -and onshore sites (in all but one case) and a ratio > 0.18 corresponded in all cases (except one) with the presence of Ca . Scalindua 16S rRNA genes. Lastly, when investigating in situ anammox, we highlight the importance of using ladderane IPLs over BHT- x and/or ladderane FAs; these latter compounds are more recalcitrant and may derive from transported fossil anammox bacteria remnants.
Subject code	333
Language	English
Publishing date	2021-10-05
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Virus production in phosphorus-limited Micromonas pusilla stimulated by a supply of naturally low concentrations of different phosphorus sources, far into the lytic cycle.

Maat, Douwe S / van Bleijswijk, Judith D L / Witte, Harry J / Brussaard, Corina P D

FEMS microbiology ecology

2016 Volume 92, Issue 9

Abstract: Earlier studies show that the proliferation of phytoplankton viruses can be inhibited by depletion of soluble reactive phosphorus (SRP; orthophosphate). In natural marine waters, phytoplankton phosphorus (P) availability is, however, largely determined ... ...

Abstract	Earlier studies show that the proliferation of phytoplankton viruses can be inhibited by depletion of soluble reactive phosphorus (SRP; orthophosphate). In natural marine waters, phytoplankton phosphorus (P) availability is, however, largely determined by the supply rate of SRP (e.g. through remineralization) and potentially by the source of P as well (i.e. the utilization of soluble non-reactive P; SNP). Here we show how a steady low supply of P (mimicking natural P recycling) to virally infected P-limited Micromonas pusilla stimulates virus proliferation. Independent of the degree of P limitation prior to infection (0.32 and 0.97μmax chemostat cultures), SRP supply resulted in 2-fold higher viral burst sizes (viruses lysed per host cell) as compared with no addition (P starvation). Delaying these spikes during the infection cycle showed that the added SRP was utilized for extra M. pusilla virus (MpV) production far into the lytic cycle (18 h post-infection). Moreover, P-limited M. pusilla utilized several SNP compounds with high efficiency and with the same extent of burst size stimulation as for SRP. Finally, addition of virus-free MpV lysate (representing a complex SNP mixture) to newly infected cells enhanced MpV production, implicating host-associated alkaline phosphatase activity, and highlighting its important role in oligotrophic environments.
MeSH term(s)	Chlorophyta/metabolism ; Chlorophyta/virology ; Phosphates/metabolism ; Phosphorus/metabolism ; Phytoplankton/metabolism ; Phytoplankton/virology ; Virus Physiological Phenomena
Chemical Substances	Phosphates ; Phosphorus (27YLU75U4W)
Language	English
Publishing date	2016-09
Publishing country	England
Document type	Journal Article
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiw136
Database	MEDical Literature Analysis and Retrieval System OnLINE

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ab Jg. 2022: Lesesaal (EG)

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Article: Strong population structure but no equilibrium yet: Genetic connectivity and phylogeography in the kelp

Luttikhuizen, Pieternella C / van den Heuvel, Freek H M / Rebours, Céline / Witte, Harry J / van Bleijswijk, Judith D L / Timmermans, Klaas

Ecology and evolution

2018 Volume 8, Issue 8, Page(s) 4265–4277

Abstract: Kelp aquaculture is globally developing steadily as human food source, along with other applications. One of the newer crop species ... ...

Abstract	Kelp aquaculture is globally developing steadily as human food source, along with other applications. One of the newer crop species is
Language	English
Publishing date	2018-04-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.3968
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge

Haalboom, Sabine / Price, David M. / Mienis, Furu / Bleijswijk, Judith D. L. / Stigter, Henko C. / Witte, Harry J. / Reichart, Gert-Jan / Duineveld, Gerard C. A.

eISSN: 1726-4189

2020

Abstract: Hydrothermal vent fields found at mid-ocean ridges emit hydrothermal fluids that disperse as neutrally buoyant plumes. From these fluids seafloor massive sulfides (SMS) deposits are formed, which are being explored as possible new mining sites for (trace) ...

Abstract	Hydrothermal vent fields found at mid-ocean ridges emit hydrothermal fluids that disperse as neutrally buoyant plumes. From these fluids seafloor massive sulfides (SMS) deposits are formed, which are being explored as possible new mining sites for (trace) metals and rare earth elements (REEs). It has been suggested that during mining activities large amounts of suspended matter will appear in the water column due to excavation processes and discharge of mining waste from the surface vessel. Understanding how hydrothermal plumes can be characterised by means of geochemistry and microbiology as they spread away from their source and how they affect their surrounding environment may help in characterising the behaviour of the dilute distal part of chemically enriched mining plumes. This study on the extensive Rainbow hydrothermal plume, observed up to 25 km downstream from the vent site, enabled us to investigate how microbial communities and (trace) metal composition change in a natural plume with distance. The (trace) metal and REE content of suspended particulate matter (SPM) was determined using sector field inductively coupled plasma mass spectrometry (SF-ICP-MS) with high resolution (HR), and the microbial communities of the neutrally buoyant plume, above-plume, below-plume, and near-bottom water and sediment were characterised by using 16S rRNA amplicon sequencing methods. Both vertically in the water column and horizontally along the neutrally buoyant plume, geochemical and biological changes were evident, as the neutrally buoyant plume stood out by its enrichments in (trace) metals and REEs, as, for example, Fe, Cu, V, Mn and REEs were enriched by factors of up to ∼80 , ∼90 , ∼52 , ∼2.5 and ∼40 , respectively, compared to above-plume water samples taken at 1000 m water depth. The concentrations of these elements changed as the plume aged, shown by the decrease in element ∕ Fe molar ratios of chalcophile elements (Cu, Co, Zn), indicative of rapid removal from the hydrothermal plume or removal from the solid phase. Conversely, increasing REE ∕ Fe molar ratios imply uptake of REEs from the ambient seawater onto Fe-oxyhydroxides. This was also reflected in the background pelagic system, as Epsilonproteobacteria started to dominate and univariate microbial biodiversity declined with distance away from the Rainbow hydrothermal vent field. The Rainbow hydrothermal plume provides a geochemically enriched natural environment, which is a heterogeneous, dynamic habitat that is conducive to ecological changes in a short time span. This study of a hydrothermal plume provides a baseline study to characterise the natural plume before the interference of deep-sea mining.
Subject code	551
Language	English
Publishing date	2020-05-12
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Virus production in phosphorus-limited Micromonas pusilla stimulated by a supply of naturally low concentrations of different phosphorus sources, far into the lytic cycle

Maat, Douwe S / van Bleijswijk, Judith D. L / Witte, Harry J / Brussaard, Corina P. D

FEMS microbiology ecology. 2016 June 16, v. 92, no. 9

2016

Abstract	Earlier studies show that the proliferation of phytoplankton viruses can be inhibited by depletion of soluble reactive phosphorus (SRP; orthophosphate). In natural marine waters, phytoplankton phosphorus (P) availability is, however, largely determined by the supply rate of SRP (e.g. through remineralization) and potentially by the source of P as well (i.e. the utilization of soluble non-reactive P; SNP). Here we show how a steady low supply of P (mimicking natural P recycling) to virally infected P-limited Micromonas pusilla stimulates virus proliferation. Independent of the degree of P limitation prior to infection (0.32 and 0.97μₘₐₓ chemostat cultures), SRP supply resulted in 2-fold higher viral burst sizes (viruses lysed per host cell) as compared with no addition (P starvation). Delaying these spikes during the infection cycle showed that the added SRP was utilized for extra M. pusilla virus (MpV) production far into the lytic cycle (18 h post-infection). Moreover, P-limited M. pusilla utilized several SNP compounds with high efficiency and with the same extent of burst size stimulation as for SRP. Finally, addition of virus-free MpV lysate (representing a complex SNP mixture) to newly infected cells enhanced MpV production, implicating host-associated alkaline phosphatase activity, and highlighting its important role in oligotrophic environments.
Keywords	alkaline phosphatase ; enzyme activity ; orthophosphates ; phytoplankton ; reactive phosphorus ; single nucleotide polymorphism ; starvation ; viruses
Language	English
Dates of publication	2016-0616
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiw136
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Cologne/Königswinter

Zs.A 2967: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Book ; Online: Successional patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge

Haalboom, Sabine / Price, David M. / Mienis, Furu / Bleijswijk, Judith D. L. / Stigter, Henko C. / Witte, Harry J. / Reichart, Gert-Jan / Duineveld, Gerard C. A.

eISSN: 1726-4189

2019

Abstract: Hydrothermal vent fields found at mid-ocean ridges emit hydrothermal fluids which disperse as neutrally buoyant plumes. From these fluids seafloor massive sulfides (SMS) deposits are formed which are being explored as possible new mining sites for (trace) ...

Abstract	Hydrothermal vent fields found at mid-ocean ridges emit hydrothermal fluids which disperse as neutrally buoyant plumes. From these fluids seafloor massive sulfides (SMS) deposits are formed which are being explored as possible new mining sites for (trace) metals and rare earth elements (REE). It has been suggested that during mining activities large amounts of suspended matter will appear in the water column due to excavation processes, and due to discharge of mining waste from the surface vessel. Understanding how natural hydrothermal plumes evolve as they spread away from their source and how they affect their surrounding environment may provide some analogies for the behaviour of the dilute distal part of chemically enriched mining plumes. This study on the extensive Rainbow hydrothermal plume, observed up to 25 km downstream from the vent site, enabled us to investigate how microbial communities change in the presence of a natural plume. The (trace) metal and REE content of suspended particulate matter (SPM) was determined using HR-ICP mass spectrometry and the microbial communities of the neutrally buoyant plume, above plume-, below plume-, and near-bottom water and sediment were characterised by using 16S rRNA amplicon sequencing methods. Both vertically in the water column and horizontally along the neutrally buoyant plume, geochemical and biological changes were evident as the neutrally buoyant plume stood out by its enrichments in (trace) metals and REEs, of which the concentrations changed as the plume aged. This was also reflected in the background pelagic system as Epsilonproteobacteria started to dominate and the biodiversity appeared to reduce with distance away from the Rainbow hydrothermal vent field. The Rainbow hydrothermal plume provides a geochemically enriched natural environment, which is a heterogeneous, dynamic habitat that is conducive to ecological changes in a short time span.
Subject code	551
Language	English
Publishing date	2019-06-20
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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