Molecular assays advance understanding of sulfate reduction despite cryptic cycles

Reese, Brandi Kiel; Witmer, Angela D.; Moller, Stacey; Morse, John W.; Mills, Heath J.

doi:10.1007/s10533-013-9933-2

Cited by 8 publications

(9 citation statements)

References 55 publications

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“…However, the technique offers a much deeper insight into different phylogenetic levels to answer more sophisticated questions, e.g., on the distribution of specific phyla with low abundance. The compiled dataset presented here, was previously published in individual studies to describe the active community compositions at the particular locations (Mills et al, 2012; Reese et al, 2013, 2014, 2018). The whole process of reanalyzing the data was only possible due to an intense collaboration between all coauthors of this study and the willingness to provide the raw data.…”

Section: Discussionmentioning

confidence: 99%

“…Sediment samples were collected at seven locations worldwide (Figure 1 and Supplementary Table S1) during various oceanographic and field expeditions between 2007 and 2012. The shallowest sites with a water depth of 3 mbsl were located in the mouth of Nueces River, near Corpus Christi Bay (Corpus Christi, TX, United States) and were sampled in 2009 as described by Reese et al (2014). Several locations within the Gulf of Mexico were sampled between 2008 and 2012 during expeditions Mechanisms Controlling Hypoxia (MCH) 11, 12, 14, 19 and 21 on board the R/V Pelican and sediments were treated as reported by Reese et al (2013).…”

Section: Methodsmentioning

confidence: 99%

“…To identify the metabolically active Rhodobacteraceae , 154 individual samples were subjected to RNA extraction and pyrosequencing of 16S rRNA transcripts. The overall community structures were previously described in several publications (Mills et al, 2012; Reese et al, 2013, 2014, 2018). Because these datasets were processed over several years, all sequences first had to run through the same bioinformatic pipeline with a unified quality control and phylogenetic reclassification.…”

Section: Introductionmentioning

confidence: 99%

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The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions

et al. 2019

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General studies on benthic microbial communities focus on fundamental biogeochemical processes or the most abundant constituents. Thereby, minor fractions such as the Rhodobacteraceae are frequently neglected. Even though this family belongs to the most widely distributed bacteria in the marine environment, their proportion on benthic microbial communities is usually within or below the single digit range. Thus, knowledge on these community members is limited, even though their absolute numbers might exceed those from the pelagic zone by orders of magnitudes. To unravel the distribution and diversity of benthic, metabolically active Rhodobacteraceae , we have now analyzed an already existing library of bacterial 16S rRNA transcripts. The dataset originated from 154 individual sediment samples comprising seven oceanic regions and a broad variety of environmental conditions. Across all samples, a total of 0.7% of all 16S rRNA transcripts was annotated as Rhodobacteraceae. Among those, Sulfitobacter , Paracoccus , and Phaeomarinomonas were the most abundant cultured representatives, but the majority (78%) was affiliated to uncultured family members. To define them, the 45 most abundant Rhodobacteraceae -OTUs assigned as “uncultured” were phylogenetically assembled in new clusters. Their next relatives particularly belonged to different subgroups other than the Roseobacter group, reflecting a large part of the hidden diversity within the benthic Rhodobacteraceae with unknown functions. The general composition of active Rhodobacteraceae communities was found to be specific for the geographical location, exhibiting a decreasing richness with sediment depth. One-third of the Rhodobacteraceae -OTUs significantly responded to the prevailing redox regime, suggesting an adaption to anoxic conditions. A possible approach to predict their physiological properties is to identify the metabolic capabilities of their nearest relatives. Those need to be proven by physiological experiments, as soon an isolate is available. Because many uncultured members of these subgroups likely thrive under anoxic conditions, in future research, a molecular-guided cultivation strategy can be pursued to isolate novel Rhodobacteraceae from sediments.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions

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“…Quantitative PCR Real-time qPCR (25 ml total volume, reaction conditions: 95 1C for 5 min, 40 cycles of 95 1C for 30 s, 48 1C for 45 s, 70 1C for 30 s standard melt curve at the end) was performed on environmental DNA extracts at depths from 5 to 175 m on an Applied Biosystems StepOnePlus Real Time PCR system and processed using StepOne Software Version 2.1 (Applied Biosystems, Foster City, CA, USA) as previously described (Reese et al, 2014). DNA was amplified with the QuantiTect SYBR Green PCR Kit (Qiagen, Valencia, CA, USA) using the KM1013-14F/R primers given in Table 1.…”

Section: Field Samplingmentioning

confidence: 99%

A novel cohabitation between two diazotrophic cyanobacteria in the oligotrophic ocean

et al. 2014

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The cyanobacterial genus Trichodesmium is biogeochemically significant because of its dual role in nitrogen and carbon fixation in the oligotrophic ocean. Trichodesmium species form colonies that can be easily enriched from the water column and used for shipboard rate measurements to estimate their contribution to oceanic carbon and nitrogen budgets. During a July 2010 cruise near the Hawaiian Islands in the oligotrophic North Pacific Subtropical Gyre, a specific morphology of Trichodesmium puff-form colonies were examined under epifluorescent microscopy and found to harbor a colonial endobiont, morphologically identified as the heterocystous diazotrophic cyanobacterium Calothrix. Using unialgal enrichments obtained from this cruise, we show that these Calothrix-like heterocystous cyanobionts (hetDA for 'Trichodesmium-associated heterocystous diazotroph') fix nitrogen on a diurnal cycle (maximally in the middle of the light cycle with a detectable minimum in the dark). Gene sequencing of nifH from the enrichments revealed that this genus was likely not quantified using currently described quantitative PCR (qPCR) primers. Guided by the sequence from the isolate, new hetDA-specific primers were designed and subsequent qPCR of environmental samples detected this diazotroph from surface water to a depth of 150 m, reaching densities up to B9 Â 10 3 l À 1 . Based on phylogenetic relatedness of nifH and 16S rRNA gene sequences, it is predicted that the distribution of this cyanobiont is not limited to subtropical North Pacific but likely reaches to the South Pacific and Atlantic Oceans. Therefore, this previously unrecognized cohabitation, if it reaches beyond the oligotrophic North Pacific, could potentially influence Trichodesmium-derived nitrogen fixation budgets in the world ocean.

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“…Many of these ASVs were putatively assigned to orders known to reduce nitrate These shifts in the community provide evidence for selection of taxa more adept at using nitrate or oxidizing more complex OM. In contrast, ASVs more abundant in the unamended treatment included orders that are ubiquitous in soil and mangrove sediments (Verrucomicrobiae, Caldithrixales;Miroshnichenko et al 2010, Freitas et al 2012, that can reduce sulfate (Desulfobacterales, Desulfarculales; , and that exhibit properties associated with iron metabolism (Campylobacterales, Rhizobiales (Eppinger et al 2004, Reese et al 2013.…”

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Nitrate as an electron acceptor in microbial decomposition of salt marsh sediment organic matter and implications for carbon storage

Bulseco-McKim¹

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I could not have had more supportive, encouraging advisors throughout my academic career thus far. First and foremost, I thank Jennifer Bowen for teaching me how to be resilient, both as a scientist and as a human. Her ability to think critically and quickly are skills I will always strive to match. More importantly, Jen has helped me persevere through times of extreme anxiety and self-doubt, and for that I will be forever grateful. I also thank my co-advisor, Anne Giblin, whose kindness and willingness to help are unmatched by any other individual I have ever met. She is an exceptional role model for women in science everywhere, and helped to shape the clarity of my work. Thank you to the rest of my committee at Northeastern University, Randall Hughes, Aron Stubbins, and Amy Mueller, who contributed insightful thought to my dissertation. I would also like to thank my UMass committee, including Bob Chen and Crystal Schaaf, who both played a critical role in the initial development of my proposal and critical thinking. Lastly, a sincere mahalo to my undergraduate advisor, Tracy Wiegner, for being my biggest cheerleader throughout the years.

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Molecular assays advance understanding of sulfate reduction despite cryptic cycles

Cited by 8 publications

References 55 publications

The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions

The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions

A novel cohabitation between two diazotrophic cyanobacteria in the oligotrophic ocean

Nitrate as an electron acceptor in microbial decomposition of salt marsh sediment organic matter and implications for carbon storage

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