Microbial Communities Promoting Mn(II) Oxidation in Ashumet Pond, a Historically Polluted Freshwater Pond Undergoing Remediation

<div><p>An extensive culture-dependent and -independent study was conducted to identify microorganisms contributing to the biogeochemical cycling of manganese (Mn) in Ashumet Pond, a freshwater pond in Massachusetts currently undergoing remediation. A variety of bacteria (including Gamma-, Beta-, and Alpha-proteobacteria, Firmicutes, and Bacteroides) and Ascoymete fungi were isolated from the pond that promote Mn(II) oxidation and subsequent formation of Mn(III/IV) oxide minerals. Targeted-amplicon pyrosequencing of the bacterial and fungal communities associated with Mn oxide-encrusted samples show a highly diverse microbial community, of which the cultured phylotypes represent a minor proportion. This suggests a larger community, not identified through culturing, contributes to Mn oxide formation within the Pond.</p></div

Table_1_Rates and pathways of iodine speciation transformations at the Bermuda Atlantic Time Series.xlsx

The distribution of iodine in the surface ocean – of which iodide-iodine is a large destructor of tropospheric ozone (O3) – can be attributed to both in situ (i.e., biological) and ex situ (i.e., mixing) drivers. Currently, uncertainty regarding the rates and mechanisms of iodide (I-) oxidation render it difficult to distinguish the importance of in situ reactions vs ex situ mixing in driving iodine’s distribution, thus leading to uncertainty in climatological ozone atmospheric models. It has been hypothesized that reactive oxygen species (ROS), such as superoxide (O2•−) or hydrogen peroxide (H2O2), may be needed for I- oxidation to occur at the sea surface, but this has yet to be demonstrated in natural marine waters. To test the role of ROS in iodine redox transformations, shipboard isotope tracer incubations were conducted as part of the Bermuda Atlantic Time Series (BATS) in the Sargasso Sea in September of 2018. Incubation trials evaluated the effects of ROS (O2•−, H2O2) on iodine redox transformations over time and at euphotic and sub-photic depths. Rates of I- oxidation were assessed using a 129I- tracer (t1/2 ~15.7 Myr) added to all incubations, and 129I/127I ratios of individual iodine species (I-, IO3-). Our results show a lack of I- oxidation to IO3- within the resolution of our tracer approach – i.e., <2.99 nM/day, or <1091.4 nM/yr. In addition, we present new ROS data from BATS and compare our iodine speciation profiles to that from two previous studies conducted at BATS, which demonstrate long-term iodine stability. These results indicate that ex situ processes, such as vertical mixing, may play an important role in broader iodine species’ distribution in this and similar regions.</p

DataSheet_1_Rates and pathways of iodine speciation transformations at the Bermuda Atlantic Time Series.pdf

The distribution of iodine in the surface ocean – of which iodide-iodine is a large destructor of tropospheric ozone (O3) – can be attributed to both in situ (i.e., biological) and ex situ (i.e., mixing) drivers. Currently, uncertainty regarding the rates and mechanisms of iodide (I-) oxidation render it difficult to distinguish the importance of in situ reactions vs ex situ mixing in driving iodine’s distribution, thus leading to uncertainty in climatological ozone atmospheric models. It has been hypothesized that reactive oxygen species (ROS), such as superoxide (O2•−) or hydrogen peroxide (H2O2), may be needed for I- oxidation to occur at the sea surface, but this has yet to be demonstrated in natural marine waters. To test the role of ROS in iodine redox transformations, shipboard isotope tracer incubations were conducted as part of the Bermuda Atlantic Time Series (BATS) in the Sargasso Sea in September of 2018. Incubation trials evaluated the effects of ROS (O2•−, H2O2) on iodine redox transformations over time and at euphotic and sub-photic depths. Rates of I- oxidation were assessed using a 129I- tracer (t1/2 ~15.7 Myr) added to all incubations, and 129I/127I ratios of individual iodine species (I-, IO3-). Our results show a lack of I- oxidation to IO3- within the resolution of our tracer approach – i.e., <2.99 nM/day, or <1091.4 nM/yr. In addition, we present new ROS data from BATS and compare our iodine speciation profiles to that from two previous studies conducted at BATS, which demonstrate long-term iodine stability. These results indicate that ex situ processes, such as vertical mixing, may play an important role in broader iodine species’ distribution in this and similar regions.</p

DataSheet_1_Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms.pdf

Certain benthic foraminifera thrive in marine sediments with low or undetectable oxygen. Potential survival avenues used by these supposedly aerobic protists include fermentation and anaerobic respiration, although details on their adaptive mechanisms remain elusive. To better understand the metabolic versatility of foraminifera, we studied two benthic species that thrive in oxygen-depleted marine sediments. Here we detail, via transcriptomics and metatranscriptomics, differential gene expression of Nonionella stella and Bolivina argentea, collected from Santa Barbara Basin, California, USA, in response to varied oxygenation and chemical amendments. Organelle-specific metabolic reconstructions revealed these two species utilize adaptable mitochondrial and peroxisomal metabolism. N. stella, most abundant in anoxia and characterized by lack of food vacuoles and abundance of intracellular lipid droplets, was predicted to couple the putative peroxisomal beta-oxidation and glyoxylate cycle with a versatile electron transport system and a partial TCA cycle. In contrast, B. argentea, most abundant in hypoxia and contains food vacuoles, was predicted to utilize the putative peroxisomal gluconeogenesis and a full TCA cycle but lacks the expression of key beta-oxidation and glyoxylate cycle genes. These metabolic adaptations likely confer ecological success while encountering deoxygenation and expand our understanding of metabolic modifications and interactions between mitochondria and peroxisomes in protists.</p

DataSheet_2_Two canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms.xlsx

Certain benthic foraminifera thrive in marine sediments with low or undetectable oxygen. Potential survival avenues used by these supposedly aerobic protists include fermentation and anaerobic respiration, although details on their adaptive mechanisms remain elusive. To better understand the metabolic versatility of foraminifera, we studied two benthic species that thrive in oxygen-depleted marine sediments. Here we detail, via transcriptomics and metatranscriptomics, differential gene expression of Nonionella stella and Bolivina argentea, collected from Santa Barbara Basin, California, USA, in response to varied oxygenation and chemical amendments. Organelle-specific metabolic reconstructions revealed these two species utilize adaptable mitochondrial and peroxisomal metabolism. N. stella, most abundant in anoxia and characterized by lack of food vacuoles and abundance of intracellular lipid droplets, was predicted to couple the putative peroxisomal beta-oxidation and glyoxylate cycle with a versatile electron transport system and a partial TCA cycle. In contrast, B. argentea, most abundant in hypoxia and contains food vacuoles, was predicted to utilize the putative peroxisomal gluconeogenesis and a full TCA cycle but lacks the expression of key beta-oxidation and glyoxylate cycle genes. These metabolic adaptations likely confer ecological success while encountering deoxygenation and expand our understanding of metabolic modifications and interactions between mitochondria and peroxisomes in protists.</p

Genome-based evaluation of unique proteins experimentally identified in secretomes of four Ascomycete fungi.

<p>Genome-based evaluation of unique proteins experimentally identified in secretomes of four Ascomycete fungi.</p

Distribution of proteins identified in secretomes of four Ascomycete fungi among broad functional groups.

<p>(A) Experimentally observed secretome. Proteins identified via LC-MS/MS over a 21-day study. (B) Portion of experimental secretome predicted to be secreted based on genome analysis (see text for further explanation). (C) Full predicted secretome based on genomes only. Total number of proteins identified for each fungus is indicated in center of circles. Abbreviations from CAZy database: AA = auxiliary activities; CBM = carbohydrate-binding module; CE = carbohydrate esterase; GH = glycoside hydrolase; GT = glucosyltransferase; PL = polysaccharide lyase.</p

Summary of identified CAZymes in secretomes of four Ascomycete fungi.

<p>Summary of identified CAZymes in secretomes of four Ascomycete fungi.</p

Venn diagram showing number of unique and shared proteins experimentally identified in Ascomycete fungi secretomes.

<p>Proteins identified via LC-MS/MS over a 21-day study. Total number of proteins identified for each fungus is indicated outside of diagram. Diagram generated with Venny 2.0 [<i>Oliveros</i>, <i>J</i>.<i>C</i>. <i>(2007–2015) Venny</i>. <i>An interactive tool for comparing lists with Venn’s diagrams. <a href="http://bioinfogp.cnb.csic.es/tools/venny/index.html" target="_blank">http://bioinfogp.cnb.csic.es/tools/venny/index.html</a></i>].</p

Distribution of proteins experimentally identified in secretomes of four Ascomycete fungi among protein families.

<p>Glycoside hydrolase families (both top and bottom panels). Solid bars: Portion of experimental secretome predicted to be secreted based on genome analysis. Shaded bars: Portion not predicted to be secreted. Proteins identified via LC-MS/MS over a 21-day study and classified according to the CAZy database. Abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157844#pone.0157844.g001" target="_blank">Fig 1</a>.</p