The effect of polyvinyl chloride (PVC) color on biofilm development and biofilm-heavy metal chemodynamics in the aquatic environment.

Plastic surfaces are colonized by microorganisms and biofilms are formed in the natural aquatic environment. As the biofilm develops, it changes the density and buoyancy of the plastic-biofilm complex, results in plastic sinking, and increases the heavy metals accumulated by biofilm's mobility and availability in aquatic ecosystems. In this experiment, biofilms were cultured on five colors of polyvinyl chloride (PVC; transparent, green, blue, red, black) in an aquatic environment to investigate the effects of plastic color on biofilm formation and development (Phase 1) and to study the effects of being sunk below the photic zone on biofilm (Phase 2). The PVC color significantly affected the biofilm formation rate but had no impact on the final biofilm biomass. After sinking the biofilm-PVC below the photic zone in Phase 2, the layer of diatoms on the biofilm surface began to disintegrate, and the biomass and Chlorophyll-a (Chla) content of the biofilm decreased, except on the red PVC. Below the photic zone, the microbial community of the biofilm changed from primarily autotrophic microbes to mostly heterotrophic microbes. Microbial diversity increased and extracellular polymeric substances (EPS) content decreased. The primary factor leading to microbial diversity and community structure changes was water depth rather than PVC color. The changes induced in the biofilm led to an increase in the concentration of all heavy metals in the biofilm, related to the increase in microbial diversity. This study provides new insights into the biofilm formation process and the effects on a biofilm when it sinks below the photic zone.

Taxonomy and morphology of Calciopappus curvus sp. nov. (Syracosphaeraceae, Prymnesiophyceae), a novel appendage-bearing coccolithophore.

Based on scanning electron microscopy observations, a new species of the coccolithophore genus Calciopappus (Syracosphaeraceae, Prymnesiophyceae) is described from the surface waters off Bergen and from the lower photic zone of sub-tropical and tropical waters. Morphological, coccolith rim structure and biometric analyses strongly support separation of this morphotype from the two described Calciopappus species, but inclusion of it within the genus. The new form differs from the other species in being noticeably smaller and in morpho-structural details of each of the three coccolith types that form the coccosphere: (1) the body coccoliths have an open central area; (2) the whorl coccoliths have a wide central opening and two thumb-like protrusions; and (3) the appendage coccoliths are curved. On this basis, the species is formally described as Calciopappus curvus sp. nov., its systematic affinity is discussed and compared with other extant coccolithophores.

The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean.

To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.

Searching Metagenomes for New Rhodopsins.

Most microbial groups have not been cultivated yet, and the only way to approach the enormous diversity of rhodopsins that they contain in a sensible timeframe is through the analysis of their genomes. High-throughput sequencing technologies have allowed the release of community genomics (metagenomics) of many habitats in the photic zones of the ocean and lakes. Already the harvest is impressive and included from the first bacterial rhodopsin (proteorhodopsin) to the recent discovery of heliorhodopsin by functional metagenomics. However, the search continues using bioinformatic or biochemical routes.

Biomarker and compound-specific isotope records across the Toarcian CIE at the Dormettingen section in SW Germany.

The Toarcian oceanic anoxic event (T-OAE) is associated with a prominent negative carbon isotope excursion (CIE; ~ 183 million years (Myr)). About 10-m-thick organic matter-rich sediments accumulated during the T-OAE in the Southwest German Basin (SWGB). Rock-Eval, maceral and biomarker analysis were used to determine variations of environmental conditions across the CIE interval. Carbon isotope records were determined for various n-alkanes, pristane and phytane to contribute to the reconstruction of the paleo-environment and to study the factors controlling molecular δ13C values. Geochemical redox indicators provide evidence for photic zone anoxia during the Toarcian CIE, which reached its maximum after deposition of the "Unterer Stein" marker horizon. The 2α-methylhopane index suggests enhanced activity of diazotrophic cyanobacteria, which is also supported by nitrogen isotope data. This distinguishes the SWGB from other basins with Toarcian black shale. Oxygen-depleted conditions, albeit with lower intensity continued after the CIE. All investigated compounds replicate the negative CIE, but the magnitudes vary considerably. The largest shift is observed for n-C27 (9‰) and reflects the combined effect of the global CIE and a major change in organic matter input (termination of terrigenous organic matter input). The shift for short-chain n-alkanes, pristane, and phytane, interpreted to reflect marine biomass, varies between 4.5 and 5.0‰. This is the highest value observed so far for any Toarcian section. δ13C values of pristane and phytane reach a minimum near the base of the CIE interval and increase upsection. Thus, the maximum negative isotope shift predates the strongest basin restriction by about 450 thousand years (kyr).

Predictive Model of Lake Photic Zone Temperature Across the Conterminous United States.

As the average global air temperature increases, lake surface temperatures are also increasing globally. The influence of this increased temperature is known to impact lake ecosystems across local to broad scales. Warming lake temperature is linked to disruptions in trophic linkages, changes in thermal stratification, and cyanobacteria bloom dynamics. Thus, comprehending broad trends in lake temperature is important to understanding the changing ecology of lakes and the potential human health impacts of these changes. To help address this, we developed a simple yet robust random forest model of lake photic zone temperature using the 2007 and 2012 United States Environmental Protection Agency's National Lakes Assessment data for the conterminous United States. The final model has a root mean square error of 1.48°C and an adjusted R2 of 0.88; the final model included 2,282 total samples. The sampling date, that day's average ambient air temperature and longitude are the most important variables impacting the final model's accuracy. The final model also included 30-days average temperature, elevation, latitude, lake area, and lake shoreline length. Given the importance of temperature to a lake ecosystem, this model can be a valuable tool for researchers and lake resource managers. Daily predicted lake photic zone temperature for all lakes in the conterminous US can now be estimated based on basic ambient temperature and location information.

Genome Analysis of a Marine Bacterium Halomonas sp. and Its Role in Nitrate Reduction under the Influence of Photoelectrons.

The solar light response and photoelectrons produced by widespread semiconducting mineral play important roles in biogeochemical cycles on Earth's surface. To explore the potential influence of photoelectrons generated by semiconducting mineral particles on nitrate-reducing microorganisms in the photic zone, a marine heterotrophic denitrifier Halomonas sp. strain 3727 was isolated from seawater in the photic zone of the Yellow Sea, China. This strain was classified as a Halomonadaceae. Whole-genome analysis indicated that this strain possessed genes encoding the nitrogen metabolism, i.e., narG, nasA, nirBD, norZ, nosB, and nxr, which sustained dissimilatory nitrate reduction, assimilatory nitrate reduction, and nitrite oxidation. This strain also possessed genes related to carbon, sulfur, and other metabolisms, hinting at its substantial metabolic flexibility. A series of microcosm experiments in a simulative photoelectron system was conducted, and the results suggested that this bacterial strain could use simulated photoelectrons with different energy for nitrate reduction. Nitrite, as an intermediate product, was accumulated during the nitrate reduction with limited ammonia residue. The nitrite and ammonia productions differed with or without different energy electron supplies. Nitrite was the main product accounting for 30.03% to 68.40% of the total nitrogen in photoelectron supplement systems, and ammonia accounted for 3.77% to 8.52%. However, in open-circuit systems, nitrite and ammonia proportions were 26.77% and 11.17%, respectively, and nitrogen loss in the liquid was not observed. This study reveals that photoelectrons can serve as electron donors for nitrogen transformation mediated by Halomonas sp. strain 3727, which reveals an underlying impact on the nitrogen biogeochemical cycle in the marine photic zone.

Niche expansion for phototrophic sulfur bacteria at the Proterozoic-Phanerozoic transition.

Fossilized carotenoid hydrocarbons provide a window into the physiology and biochemistry of ancient microbial phototrophic communities for which only a sparse and incomplete fossil record exists. However, accurate interpretation of carotenoid-derived biomarkers requires detailed knowledge of the carotenoid inventories of contemporary phototrophs and their physiologies. Here we report two distinct patterns of fossilized C40 diaromatic carotenoids. Phanerozoic marine settings show distributions of diaromatic hydrocarbons dominated by isorenieratane, a biomarker derived from low-light-adapted phototrophic green sulfur bacteria. In contrast, isorenieratane is only a minor constituent within Neoproterozoic marine sediments and Phanerozoic lacustrine paleoenvironments, for which the major compounds detected are renierapurpurane and renieratane, together with some novel C39 and C38 carotenoid degradation products. This latter pattern can be traced to cyanobacteria as shown by analyses of cultured taxa and laboratory simulations of sedimentary diagenesis. The cyanobacterial carotenoid synechoxanthin, and its immediate biosynthetic precursors, contain thermally labile, aromatic carboxylic-acid functional groups, which upon hydrogenation and mild heating yield mixtures of products that closely resemble those found in the Proterozoic fossil record. The Neoproterozoic-Phanerozoic transition in fossil carotenoid patterns likely reflects a step change in the surface sulfur inventory that afforded opportunities for the expansion of phototropic sulfur bacteria in marine ecosystems. Furthermore, this expansion might have also coincided with a major change in physiology. One possibility is that the green sulfur bacteria developed the capacity to oxidize sulfide fully to sulfate, an innovation which would have significantly increased their capacity for photosynthetic carbon fixation.

Mercury isotope signatures record photic zone euxinia in the Mesoproterozoic ocean.

Photic zone euxinia (PZE) is a condition where anoxic, H2S-rich waters occur in the photic zone (PZ). PZE has been invoked as an impediment to the evolution of complex life on early Earth and as a kill mechanism for Phanerozoic mass extinctions. Here, we investigate the potential application of mercury (Hg) stable isotopes in marine sedimentary rocks as a proxy for PZE by measuring Hg isotope compositions in late Mesoproterozoic (∼1.1 Ga) shales that have independent evidence of PZE during discrete intervals. Strikingly, a significantly negative shift of Hg mass-independent isotope fractionation (MIF) was observed during euxinic intervals, suggesting changes in Hg sources or transformations in oceans coincident with the development of PZE. We propose that the negative shift of Hg MIF was most likely caused by (i) photoreduction of Hg(II) complexed by reduced sulfur ligands in a sulfide-rich PZ, and (ii) enhanced sequestration of atmospheric Hg(0) to the sediments by thiols and sulfide that were enriched in the surface ocean as a result of PZE. This study thus demonstrates that Hg isotope compositions in ancient marine sedimentary rocks can be a promising proxy for PZE and therefore may provide valuable insights into changes in ocean chemistry and its impact on the evolution of life.

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment.

BACKGROUND: The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment. RESULTS: Our results showed significant differences in the microbial composition of different layers within the stratified photic water column. The majority of microorganisms were confined to discreet horizontal layers of no more than 30 m (stenobathic). Only a few such as members of the SAR11 clade appeared at all depths (eurybathic). During the winter mixing period, only some groups of bloomers such as Pseudomonas were favored. Although most microbes appeared in both seasons, some groups like the SAR116 clade and some Bacteroidetes and Verrucomicrobia seemed to disappear during the mixing period. Furthermore, we found that some microbes previously considered seasonal (e.g., Archaea or Actinobacteria) were living in deeper layers within the photic zone during the stratification period. A strong depth-related specialization was detected, not only at the taxonomic level but also at the functional level, even within the different clades, for the manipulation and uptake of specific polysaccharides. Rhodopsin sequences (green or blue) also showed narrow depth distributions that correlated with the taxonomy of the microbe in which they were found but not with depth. CONCLUSIONS: Although limited to a single location in the Mediterranean, this study has profound implications for our understanding of how marine microbial communities vary with depth within the photic zone when stratified. Our results highlight the importance of collecting samples at different depths in the water column when comparing seasonal variations and have important ramifications for global marine studies that most often take samples from only one single depth. Furthermore, our perspective and approaches (metagenomic assembly and recruitment) are broadly applicable to other metagenomic studies.