Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: <scp>D</scp>evil's <scp>H</scp>ole, <scp>B</scp>ermuda

Parsons, Rachel; Nelson, Craig E.; Carlson, Craig A.; Denman, Carmen C.; Andersson, Andréas; Kledzik, Andrew L.; Vergin, Kevin L.; McNally, Sean; Treusch, Alexander H.; Giovannoni, Stephen J.

doi:10.1111/1462-2920.12445

Cited by 25 publications

(54 citation statements)

References 98 publications

(149 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Upon analysis, the samples were thawed and filtered onto 0.2 µm filters pre-stained with Irgalan black (0.2 g in 2% acetic acid) under gentle vacuum (~100 mm Hg) and post-stained with 4, 6-diamidino-2-phenyl dihydro chloride (DAPI; 5 µg ml −1 , SIGMAAldrich) (Porter & Feig 1980). Slides were then enumerated using an AX70 epifluorescent microscope (Olympus) under UV excitation at 100× magnification as previously described (Parsons et al 2014). At least 500 cells filter −1 (12 fields) were counted.…”

Section: Microbial Abundances and Fishmentioning

confidence: 99%

“…Image analysis coupled with epifluorescence micro scopy was used to process FISH slides excited with Cy3 (550 nm) and UV wavelengths. The images were captured using a Retiga Exi CCD digital camera with QCapture software (v.2.0; QImaging) and processed with Image Pro software (v.7.0; Media Cybernetics) as previously described (Parsons et al 2014). SAR11 percentages were calculated as SAR11 FISH abundances compared to total cellular abundances.…”

Section: Microbial Abundances and Fishmentioning

confidence: 99%

See 1 more Smart Citation

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

Apprill

McNally²,

Parsons³

et al. 2015

Aquat. Microb. Ecol.

1,911

1,257

View full text Add to dashboard Cite

High-throughput sequencing of small subunit ribosomal RNA (SSU rRNA) genes from marine environments is a widely applied method used to uncover the composition of microbial communities. We conducted an analysis of surface ocean waters with the commonly employed hypervariable 4 region SSU rRNA gene primers 515F and 806R, and found that bacteria belonging to the SAR11 clade of Alphaproteobacteria, a group typically making up 20 to 40% of the bacterioplankton in this environment, were greatly underrepresented and comprised < 4% of the total community. Using the SILVA reference database, we found a single nucleotide mismatch to nearly all SAR11 subclades, and revised the 806R primer so that it increased the detection of SAR11 clade sequences in the database from 2.6 to 96.7%. We then compared the performance of the original and revised 806R primers in surface seawater samples, and found that SAR11 comprised 0.3 to 3.9% of sequences with the original primers and 17.5 to 30.5% of the sequences with the revised 806R primer. Furthermore, an investigation of seawater obtained from aquaria revealed that SAR11 sequences acquired with the revised 806R primer were more similar to natural cellular abundances of SAR11 detected using fluorescence in situ hybridization counts. Collectively, these results demonstrate that a minor adjustment to the 806R primer will greatly increase detection of the globally abundant SAR11 clade in marine and lake environments, and enable inclusion of this important bacterial lineage in experimental and environmental-based studies.

show abstract

Section: Microbial Abundances and Fishmentioning

confidence: 99%

Section: Microbial Abundances and Fishmentioning

confidence: 99%

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

Apprill

McNally²,

Parsons³

et al. 2015

Aquat. Microb. Ecol.

1,911

1,257

View full text Add to dashboard Cite

show abstract

“…Summertime water column stratification typically results in seasonal hypoxia and anoxia in the bottommost 2-m depth of Devil's Hole (e.g., Coull, 1969;Beers and Herman, 1969;Thorstenson and Mackenzie, 1974;Brown, 1978Brown, , 1980Andersson et al, 2007;Parsons et al, 2015). As such, Devil's Hole has been the focus of studies of CaCO 3 sediment dissolution (e.g., Berner, 1966;Lyons et al, 1974;Balzer and Wefer, 1981;Hines and Lyons, 1982;Andersson et al, 2007), nitrogen cycling (Brown, 1981), trace-element cycling (Jickells and Knap, 1984), and microbial community changes (Coull, 1969;Parsons et al, 2015). The sediment and benthos of Harrington Sound exhibits zonation (Neumann, 1965) with a shallow sandy zone (0-10 m), a stony coral zone of Oculina sp.…”

Section: Sampling Locationsmentioning

confidence: 99%

“…Dr. Doug Connolly, Dr. Richard J. Owens, Prof. Anthony H. Knap, and Tim Noyes are thanked for the opportunities to sample Bermuda inshore waters over the past 20 years. Dr. Andreas J. Andersson is thanked for the use of data sampled at Harrington Sound in September 2008 that were published in Parsons et al (2015). These water samples were analyzed for DIC and TA in the laboratory of NB at BIOS.…”

Section: Acknowledgmentsmentioning

confidence: 99%

“…Secondly, seasonal changes in CO 2 -carbonate chemistry of surface and deeper waters (25 m) are determined as a prerequisite for examining longer-term changes. The deeper waters of Harrington Sound typically become seasonally anoxic in summertime at the water-sediment interface (e.g., Coull, 1969;Beers and Herman, 1969;Thorstenson and Mackenzie, 1974;Andersson et al, 2007;Parsons et al, 2015), thereby providing insights into the synergies between deoxygenation and OA forcing. 3.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Twenty Years of Marine Carbon Cycle Observations at Devils Hole Bermuda Provide Insights into Seasonal Hypoxia, Coral Reef Calcification, and Ocean Acidification

Bates

2017

Front. Mar. Sci.

View full text Add to dashboard Cite

Open-ocean observations have revealed gradual changes in seawater carbon dioxide (CO 2 ) chemistry resulting from uptake of atmospheric CO 2 and ocean acidification (OA), but, with few long-term records (>5 years) of the coastal ocean that can reveal the pace and direction of environmental change. In this paper, observations collected from 1996 to 2016 at Harrington Sound, Bermuda, constitute one of the longest time-series of coastal ocean inorganic carbon chemistry. Uniquely, such changes can be placed into the context of contemporaneous offshore changes observed at the nearby Bermuda Atlantic Time-series Study (BATS) site. Onshore, surface dissolved inorganic carbon (DIC) and partial pressure of CO 2 (pCO 2 ; >10% change per decade) have increased and OA indicators such as pH and calcium carbonate (CaCO 3 ) saturation state ( ) decreased from 1996 to 2016 at a rate of two to three times that observed offshore at BATS. Such changes, combined with reduction of total alkalinity over time, reveal a complex interplay of biogeochemical processes influencing Bermuda reef metabolism, including net ecosystem production (NEP = gross primary production-autotrophic and heterotrophic respiration) and net ecosystem calcification (NEC = gross calcification-gross CaCO 3 dissolution). These long-term data show a seasonal shift between wintertime net heterotrophy and summertime net autotrophy for the entire Bermuda reef system. Over annual time-scales, the Bermuda reef system does not appear to be in trophic balance, but rather slightly net heterotrophic. In addition, the reef system is net accretive (i.e., gross calcification > gross CaCO 3 dissolution), but there were occasional periods when the entire reef system appears to transiently shift to net dissolution. A previous 5-year study of the Bermuda reef suggested that net calcification and net heterotrophy have both increased. Over the past 20 years, rates of net calcification and net heterotrophy determined for the Bermuda reef system have increased by ∼30%, most likely due to increased coral nutrition occurring in concert with increased offshore productivity in the surrounding subtropical North Atlantic Ocean. Importantly, this long-term study reveals that other environmental factors (such as coral feeding) can mitigate against the effects of ocean acidification on coral reef calcification, at least over the past couple of decades.

show abstract

Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition

McNally

Parsons

Santoro

et al. 2016

Limnology & Oceanography

Self Cite

View full text Add to dashboard Cite

Picoplankton foster essential recycling of nutrients in the oligotrophic waters sustaining coral reef ecosystems. Despite this fact, there is a paucity of data on how the specific interactions between corals and planktonic bacteria and archaea (picoplankton) contribute to nutrient dynamics and reef productivity. Here, we utilized mesocosm experiments to investigate how corals and coral mucus influence picoplankton and nutrients in reef waters. Over 12 days, we tracked nutrient concentrations, picoplankton abundances and taxonomic composition of picoplankton using direct cell-counts, sequencing of SSU rRNA genes and fluorescent in situ hybridization-based abundances of dominant lineages in the presence or absence of Porites astreoides corals and with mucus additions. Our results demonstrate that when corals are present, Synechococcus, SAR11 and Rhodobacteraceae cells are preferentially removed. When corals were removed, their exudates enhanced the growth of diverse picoplankton, including SAR11 and Rhodobacteraceae. A seven-fold increase in nitrate concentration, possibly caused by nitrogen remineralization (ammonification coupled to nitrification) within the coral holobiont, may have further facilitated the growth of these taxa. In contrast, the addition of mucus resulted in rapid initial growth of total picoplankton and Rhodobacteraceae, but no measurable change in overall community structure. This study presents evidence of the multifaceted influences of corals on picoplankton, in which the coral holobiont selectively removes and promotes the growth of diverse picoplankton and remineralizes nitrogen.

show abstract

Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil's Hole, Bermuda

Cited by 25 publications

References 98 publications

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

Twenty Years of Marine Carbon Cycle Observations at Devils Hole Bermuda Provide Insights into Seasonal Hypoxia, Coral Reef Calcification, and Ocean Acidification

Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition

Contact Info

Product

Resources

About