scholarly journals Ubiquitous Dissolved Inorganic Carbon Assimilation by Marine Bacteria in the Pacific Northwest Coastal Ocean as Determined by Stable Isotope Probing

PLoS ONE ◽  
2012 ◽  
Vol 7 (10) ◽  
pp. e46695 ◽  
Author(s):  
Suzanne DeLorenzo ◽  
Suzanna L. Bräuer ◽  
Chelsea A. Edgmont ◽  
Lydie Herfort ◽  
Bradley M. Tebo ◽  
...  
2014 ◽  
Vol 41 (3) ◽  
pp. 1005-1011 ◽  
Author(s):  
Sayaka Yasunaka ◽  
Yukihiro Nojiri ◽  
Shin-ichiro Nakaoka ◽  
Tsuneo Ono ◽  
Hitoshi Mukai ◽  
...  

2020 ◽  
Vol 86 (7) ◽  
Author(s):  
Laurey Steinke ◽  
Gordon W. Slysz ◽  
Mary S. Lipton ◽  
Christian Klatt ◽  
James J. Moran ◽  
...  

ABSTRACT The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with [13C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with 13C. Most 13C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower [13C]bicarbonate incorporation. IMPORTANCE Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of 13C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13C/12C ratios of mat biomass will help geochemists interpret the 13C/12C ratios of organic carbon in the fossil record.


2017 ◽  
Vol 14 (21) ◽  
pp. 4949-4963 ◽  
Author(s):  
Andrew Joesoef ◽  
David L. Kirchman ◽  
Christopher K. Sommerfield ◽  
Wei-Jun Cai

Abstract. Carbonate geochemistry research in large estuarine systems is limited. More work is needed to understand how changes in land-use activity influence watershed export of organic and inorganic carbon, acids, and nutrients to the coastal ocean. To investigate the seasonal variation of the inorganic carbon system in the Delaware Estuary, one of the largest estuaries along the US east coast, dissolved inorganic carbon (DIC), total alkalinity (TA), and pH were measured along the estuary from June 2013 to April 2015. In addition, DIC, TA, and pH were periodically measured from March to October 2015 in the nontidal freshwater Delaware, Schuylkill, and Christina rivers over a range of discharge conditions. There were strong negative relationships between river TA and discharge, suggesting that changes in HCO3− concentrations reflect dilution of weathering products in the drainage basin. The ratio of DIC to TA, an understudied but important property, was high (1.11) during high discharge and low (0.94) during low discharge, reflecting additional DIC input in the form of carbon dioxide (CO2), most likely from terrestrial organic matter decomposition, rather than bicarbonate (HCO3−) inputs due to drainage basin weathering processes. This is also a result of CO2 loss to the atmosphere due to rapid water transit during the wet season. Our data further show that elevated DIC in the Schuylkill River is substantially different than that in the Delaware River. Thus, tributary contributions must be considered when attributing estuarine DIC sources to the internal carbon cycle versus external processes such as drainage basin mineralogy, weathering intensity, and discharge patterns. Long-term records in the Delaware and Schuylkill rivers indicate shifts toward higher alkalinity in estuarine waters over time, as has been found in other estuaries worldwide. Annual DIC input flux to the estuary and export flux to the coastal ocean are estimated to be 15.7 ± 8.2  ×  109 mol C yr−1 and 16.5 ± 10.6  ×  109 mol C yr−1, respectively, while net DIC production within the estuary including inputs from intertidal marshes is estimated to be 5.1  ×  109 mol C yr−1. The small difference between riverine input and export flux suggests that, in the case of the Delaware Estuary and perhaps other large coastal systems with long freshwater residence times, the majority of the DIC produced in the estuary by biological processes is exchanged with the atmosphere rather than exported to the sea.


2020 ◽  
Author(s):  
Xiuran Yin ◽  
Mingwei Cai ◽  
Yang Liu ◽  
Guowei Zhou ◽  
Tim Richter-Heitmann ◽  
...  

Abstract Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus ‘Prometheoarchaeum syntrophicum’. Here, we tracked the activity of Lokiarchaeota in incubations with Helgoland mud area sediments (North Sea) by stable isotope probing (SIP) with organic polymers, 13C-labelled inorganic carbon, fermentation intermediates and proteins. Within the active archaea, we detected members of the Lokiarchaeota class Loki-3, which appeared to mixotrophically participate in the degradation of lignin and humic acids while assimilating CO2, or heterotrophically used lactate. In contrast, members of the Lokiarchaeota class Loki-2 utilized protein and inorganic carbon, and degraded bacterial biomass formed in incubations. Metagenomic analysis revealed pathways for lactate degradation, and involvement in aromatic compound degradation in Loki-3, while the less globally distributed Loki-2 instead rely on protein degradation. We conclude that Lokiarchaeotal subgroups vary in their metabolic capabilities despite overlaps in their genomic equipment, and suggest that these subgroups occupy different ecologic niches in marine sediments.


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