Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology

Haas, Andreas F.; Knowles, Ben; Lim, Yan Wei; Somera, Tracey McDole; Kelly, Linda Wegley; Hatay, Mark; Rohwer, Forest

doi:10.3791/52131

Cited by 25 publications

(27 citation statements)

References 46 publications

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“…For both water column datasets, approximately 60 l of water was collected just below the ocean surface. Microbial cells from the seawater were concentrated using tangential flow filtration (Dinsdale et al ., ; Haas et al ., ), collected on 0.22 μm Sterivex filters (EMD Millipore, Billerica, MA), and frozen at −20°C until DNA extraction.…”

Section: Methodsmentioning

confidence: 99%

The skin microbiome of the common thresher shark (Alopias vulpinus) has low taxonomic and gene function β‐diversity

Doane

Haggerty

Kacev

et al. 2017

Environ Microbiol Rep

132

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Summary The health of sharks, like all organisms, is linked to their microbiome. At the skin interface, sharks have dermal denticles that protrude above the mucus, which may affect the types of microbes that occur here. We characterized the microbiome from the skin of the common thresher shark (Alopias vulpinus) to investigate the structure and composition of the skin microbiome. On average 618 812 (80.9% ± S.D. 0.44%) reads per metagenomic library contained open reading frames; of those, between 7.6% and 12.8% matched known protein sequences. Genera distinguishing the A. vulpinus microbiome from the water column included, Pseudoalteromonas (12.8% ± 4.7 of sequences), Erythrobacter (5. 3% ± 0.5) and Idiomarina (4.2% ± 1.2) and distinguishing gene pathways included, cobalt, zinc and cadmium resistance (2.2% ± 0.1); iron acquisition (1.2% ± 0.1) and ton/tol transport (1.3% ± 0.08). Taxonomic community overlap (100 – dissimilarity index) was greater in the skin microbiome (77.6), relative to the water column microbiome (70.6) and a reference host‐associated microbiome (algae: 71.5). We conclude the A. vulpinus skin microbiome is influenced by filtering processes, including biochemical and biophysical components of the shark skin and result in a structured microbiome.

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Section: Methodsmentioning

confidence: 99%

The skin microbiome of the common thresher shark (Alopias vulpinus) has low taxonomic and gene function β‐diversity

Doane

Haggerty

Kacev

et al. 2017

Environ Microbiol Rep

132

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“…Two PCR reactions (Reaction B: TTTW[I/V]W_fwd – HHIHAF_rev; Reaction L: MPPY[P/A]Y_fwd – TTW[A/S]FF_rev) were performed directly on viral concentrates from the Pacific Southern Line Islands [collected in April 2009 and in November 2013 from Caroline island (Millennium Island) and in October 2013 from Vostok Island]. Viral concentrates were prepared according to Haas and colleagues (). The PCR reactions B and L were performed using BIO‐X‐ACT TM Short mix (Bioline, London, UK), in a total volume of 30 μl containing 1 μl of phage concentrate as template, OptiBuffer (1×), 2 μM primers (each), 0.8 mM dNTPs, 2 mM MgCl 2 and 2.4 U BIO‐X‐ACT TM Short DNA polymerase.…”

Section: Methodsmentioning

confidence: 99%

Closing the gaps on the viral photosystem‐I psaDCAB gene organization

Roitman

Flores‐Uribe

Philosof

et al. 2015

Environmental Microbiology

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SummaryMarine photosynthesis is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding for photosystem (PS) I and II reaction centre proteins are found in cyanophages and are believed to increase their fitness. Two viral PSI gene arrangements are known, psaJF→C→A→B→K→E→D and psaD→C→A→B. The shared genes between these gene cassettes and their encoded proteins are distinguished by %G + C and protein sequence respectively. The data on the psaD→C→A→B gene organization were reported from only two partial gene cassettes coming from Global Ocean Sampling stations in the Pacific and Indian oceans. Now we have extended our search to 370 marine stations from six metagenomic projects. Genes corresponding to both PSI gene arrangements were detected in the Pacific, Indian and Atlantic oceans, confined to a strip along the equator (30°N and 30°S). In addition, we found that the predicted structure of the viral PsaA protein from the psaD→C→A→B organization contains a lumenal loop conserved in PsaA proteins from Synechococcus, but is completely absent in viral PsaA proteins from the psaJF→C→A→B→K→E→D gene organization and most Prochlorococcus strains. This may indicate a co‐evolutionary scenario where cyanophages containing either of these gene organizations infect cyanobacterial ecotypes biogeographically restricted to the 30°N and 30°S equatorial strip.

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“…Seawater for all four treatments was initially filtered through a 2.00 μm mesh filter to remove larger eukaryotes that could graze on the spores. Microbial density was adjusted by tangential flow filtration (TFF) to remove microbial cells from the filtrate water fraction (100 kDa pore size), while increasing microbial cell abundance in the retentate fraction (Haas et al, 2014). Seawater for the ‘low’ treatment was collected from the TFF filtrate where microbes were removed.…”

Section: Methodsmentioning

confidence: 99%

“…Filters were mounted on slides and stored at -20°C. Cell abundance was counted in replicate using ImagePro Software (Media Cybernetics, Rockville, MD, USA) for cell size range 0.20–10.00 μm (McDole et al, 2012; Haas et al, 2014). …”

Section: Methodsmentioning

confidence: 99%

Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera

et al. 2016

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Marine microbes mediate key ecological processes in kelp forest ecosystems and interact with macroalgae. Pelagic and biofilm-associated microbes interact with macroalgal propagules at multiple stages of recruitment, yet these interactions have not been described for Macrocystis pyrifera. Here we investigate the influence of microbes from coastal environments on recruitment of giant kelp, M. pyrifera. Through repeated laboratory experiments, we tested the effects of altered pelagic microbial abundance on the settlement and development of the microscopic propagules of M. pyrifera during recruitment. M. pyrifera zoospores were reared in laboratory microcosms exposed to environmental microbial communities from seawater during the complete haploid stages of the kelp recruitment cycle, including zoospore release, followed by zoospore settlement, to gametophyte germination and development. We altered the microbial abundance states differentially in three independent experiments with repeated trials, where microbes were (a) present or absent in seawater, (b) altered in community composition, and (c) altered in abundance. Within the third experiment, we also tested the effect of nearshore versus offshore microbial communities on the macroalgal propagules. Distinct pelagic microbial communities were collected from two southern California temperate environments reflecting contrasting intensity of human influence, the nearshore Point Loma kelp forest and the offshore Santa Catalina Island kelp forest. The Point Loma kelp forest is a high impacted coastal region adjacent to the populous San Diego Bay; whereas the kelp forest at Catalina Island is a low impacted region of the Channel Islands, 40 km offshore the southern California coast, and is adjacent to a marine protected area. Kelp gametophytes reared with nearshore Point Loma microbes showed lower survival, growth, and deteriorated morphology compared to gametophytes with the offshore Catalina Island microbial community, and these effects were magnified under high microbial abundances. Reducing abundance of Point Loma microbes restored M. pyrifera propagule success. Yet an intermediate microbial abundance was optimal for kelp propagules reared with Catalina Island microbes, suggesting that microbes also have a beneficial influence on kelp. Our study shows that pelagic microbes from nearshore and offshore environments are differentially influencing kelp propagule success, which has significant implications for kelp recruitment and kelp forest ecosystem health.

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Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology

Cited by 25 publications

References 46 publications

The skin microbiome of the common thresher shark (Alopias vulpinus) has low taxonomic and gene function β‐diversity

The skin microbiome of the common thresher shark (Alopias vulpinus) has low taxonomic and gene function β‐diversity

Closing the gaps on the viral photosystem‐I psaDCAB gene organization

Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera

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