scholarly journals The influence of light and water mass on bacterial population dynamics in the Amundsen Sea Polynya

Elem Sci Anth ◽  
2015 ◽  
Vol 3 ◽  
Author(s):  
Inga Richert ◽  
Julie Dinasquet ◽  
Ramiro Logares ◽  
Lasse Riemann ◽  
Patricia L. Yager ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Organic Carbon ◽  
Southern Ocean ◽  
Austral Summer ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Environmental Drivers ◽  
Nutrient Loads ◽  
Amundsen Sea ◽  
Bacterial Populations

Abstract Despite being perpetually cold, seasonally ice-covered and dark, the coastal Southern Ocean is highly productive and harbors a diverse microbiota. During the austral summer, ice-free coastal patches (or polynyas) form, exposing pelagic organisms to sunlight, triggering intense phytoplankton blooms. This strong seasonality is likely to influence bacterioplankton community composition (BCC). For the most part, we do not fully understand the environmental drivers controlling high-latitude BCC and the biogeochemical cycles they mediate. In this study, the Amundsen Sea Polynya was used as a model system to investigate important environmental factors that shape the coastal Southern Ocean microbiota. Population dynamics in terms of occurrence and activity of abundant taxa was studied in both environmental samples and microcosm experiments by using 454 pyrosequencing of 16S rRNA genes. We found that the BCC in the photic epipelagic zone had low richness, with dominant bacterial populations being related to taxa known to benefit from high organic carbon and nutrient loads (copiotrophs). In contrast, the BCC in deeper mesopelagic water masses had higher richness, featuring taxa known to benefit from low organic carbon and nutrient loads (oligotrophs). Incubation experiments indicated that direct impacts of light and competition for organic nutrients are two important factors shaping BCC in the Amundsen Sea Polynya.

scholarly journals Characteristics of biogenically-derived aerosols over the Amundsen Sea, Antarctica

2019 ◽  
Author(s):  
Jinyoung Jung ◽  
Sang-Bum Hong ◽  
Meilian Chen ◽  
Jin Hur ◽  
Liping Jiao ◽  
...  
Keyword(s):  
Biological Activity ◽  
Organic Carbon ◽  
Southern Ocean ◽  
Sea Water ◽  
Austral Summer ◽  
Water Soluble ◽  
Fluorescence Excitation ◽  
Amundsen Sea ◽  
Marine Biological ◽  
Carbon Species

Abstract. To investigate the influence of marine biological activity on aerosols, aerosol and seawater samples were collected over the Southern Ocean (43° S−70° S) and the Amundsen Sea (70° S−75° S) during the ANA06B cruise conducted in the austral summer of 2016 aboard the Korean icebreaker IBR/V Araon. Over the Southern Ocean, atmospheric methanesulfonic acid (MSA) concentration was low (0.10 ± 0.002 µg m−3), whereas its concentration increased sharply up to 0.57 µg m−3 in the Amundsen Sea where Phaeocystis antarctica (P. antarctica), a producer of dimethylsulfide (DMS), was the dominant phytoplankton species. Unlike MSA, mean non-sea-salt sulfate (nss-SO42−) concentration in the Amundsen Sea was comparable to that in the Southern Ocean, suggesting significant influences of marine biological activity on atmospheric sulfur species in the Amundsen Sea. Water-soluble organic carbon (WSOC) concentrations over the Southern Ocean and the Amundsen Sea varied from 0.048–0.16 µgC m−3 and 0.070–0.18 µgC m−3, with averages of 0.087 ± 0.038 µgC m−3 and 0.097 ± 0.038 µgC m−3, respectively. For water-insoluble organic carbon (WIOC), its mean concentrations over the Southern Ocean and the Amundsen Sea were 0.25 ± 0.13 µgC m−3 and 0.26 ± 0.10 µgC m−3, varying from 0.083–0.49 µgC m−3 and 0.12–0.38 µgC m−3, respectively. WIOC was the dominant organic carbon species in both the Southern Ocean and the Amundsen Sea, accounting for 73–75 % of total aerosol organic carbon. WSOC and WIOC were highly enriched in the submicron sea spray particles, especially in the Amundsen Sea where biological productivity was much higher than the Southern Ocean. In addition, the submicron WIOC concentration was quite related to the relative biomass of P. antarctica, suggesting that extracellular polysaccharide mucus produced by P. antarctica was a significant factor affecting atmospheric WIOC concentration in the Amundsen Sea. The fluorescence properties of WSOC investigated using fluorescence excitation-emission matrix coupled with parallel factor analysis (EEM-PARAFAC) revealed that protein-like components were dominant in our marine aerosol samples, representing 69–91 % of the total intensity. Protein-like components also showed positive relationships with the relative biomass of diatoms; however, they were negatively correlated with the relative biomass of P. antarctica. These results suggest that protein-like components are most likely produced as a result of biological processes of diatoms, which play a crucial role in forming the submicron WSOC observed over the Southern Ocean and the Amundsen Sea, and that phytoplankton community structure is a significant factor affecting atmospheric organic carbon species. The results from this study provide significant new observational data on biogenically-derived sulfur and organic carbon species in the Amundsen Sea.

scholarly journals Characteristics of methanesulfonic acid, non-sea-salt sulfate and organic carbon aerosols over the Amundsen Sea, Antarctica

2020 ◽  
Vol 20 (9) ◽  
pp. 5405-5424 ◽  
Author(s):  
Jinyoung Jung ◽  
Sang-Bum Hong ◽  
Meilian Chen ◽  
Jin Hur ◽  
Liping Jiao ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Southern Ocean ◽  
Methanesulfonic Acid ◽  
Austral Summer ◽  
Sea Salt ◽  
Water Soluble ◽  
Fluorescence Excitation ◽  
Amundsen Sea ◽  
Phaeocystis Antarctica ◽  
Seawater Samples

Abstract. To investigate the characteristics of particulate methanesulfonic acid (MSA(p)), non-sea-salt sulfate (nss SO42-) and organic carbon (OC) aerosols, aerosol and seawater samples were collected over the Southern Ocean (43–70∘ S) and the Amundsen Sea (70–75∘ S) during the ANA06B cruise conducted in the austral summer of 2016 aboard the Korean icebreaker IBR/V Araon. Over the Southern Ocean, the atmospheric MSA(p) concentration was low (0.10±0.002 µg m−3), whereas its concentration increased sharply up to 0.57 µg m−3 in the Amundsen Sea where Phaeocystis antarctica (P. antarctica), a producer of dimethylsulfide (DMS), was the dominant phytoplankton species. Unlike MSA(p), the mean nss SO42- concentration in the Amundsen Sea was comparable to that in the Southern Ocean. Water-soluble organic carbon (WSOC) concentrations over the Southern Ocean and the Amundsen Sea varied from 0.048 to 0.16 and 0.070 to 0.18 µgC m−3, with averages of 0.087±0.038 and 0.097±0.038 µgC m−3, respectively. For water-insoluble organic carbon (WIOC), its mean concentrations over the Southern Ocean and the Amundsen Sea were 0.25±0.13 and 0.26±0.10 µgC m−3, varying from 0.083 to 0.49 and 0.12 to 0.38 µgC m−3, respectively. WIOC was the dominant organic carbon species in both the Southern Ocean and the Amundsen Sea, accounting for 73 %–75 % of the total aerosol organic carbon. WSOC/Na+ and WIOC/Na+ ratios in the fine-mode aerosol particles were higher, especially in the Amundsen Sea where biological productivity was much higher than the Southern Ocean. The fluorescence properties of water-soluble organic aerosols investigated using a fluorescence excitation–emission matrix coupled with parallel factor analysis (EEM–PARAFAC) revealed that protein-like components were dominant in our marine aerosol samples, representing 69 %–91 % of the total intensity. Protein-like components also showed a significant positive relationship with the relative biomass of diatoms; however, they were negatively correlated with the relative biomass of P. antarctica. These results suggest that the protein-like component is most likely produced as a result of biological processes of diatoms in the Amundsen Sea.

Pyrosequencing analysis of free-living and attached bacterial communities in Meiliang Bay, Lake Taihu, a large eutrophic shallow lake in China

2015 ◽  
Vol 61 (1) ◽  
pp. 22-31 ◽  
Author(s):  
Xiangming Tang ◽  
Linlin Li ◽  
Keqiang Shao ◽  
Boweng Wang ◽  
Xianlei Cai ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Lake Taihu ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Eutrophic Lakes ◽  
Free Living ◽  
Bacterial Populations ◽  
Meiliang Bay ◽  
Taxonomic Groups ◽  
High Level

To elucidate the relationship between particle-attached (PA, ≥5.0 μm) and free-living (FL, 0.2–5.0 μm) bacterial communities, samplings were collected seasonally from November 2011 to August 2012 in Meiliang Bay, Lake Taihu, China. We used 454 pyrosequencing of 16S rRNA genes to study bacterial diversity and structure of PA and FL communities. The analysis rendered 37 985 highly qualified reads, subsequently assigned to 1755 operational taxonomic units (97% similarity) for the 8 samples. Although 27 high-level taxonomic groups were obtained, the 3 dominant phyla (Proteobacteria, Actinobacteria, and Bacteroidetes) comprised about 75.9% and 82.4% of the PA and FL fractions, respectively. Overall, we found no significant differences between community types, as indicated by ANOSIM R statistics (R = 0.063, P > 0.05) and the Parsimony test (P = 0.222). Dynamics of bacterial communities were correlated with changes in concentrations of total suspended solids (TSS) and total phosphorus (TP). In summer, a significant taxonomic overlap in the 2 size fractions was observed when Cyanobacteria, a major contributor of TSS and TP, dominated in the water, highlighting the potential rapid exchange between PA and FL bacterial populations in large shallow eutrophic lakes.

scholarly journals Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns

2013 ◽  
Vol 79 (11) ◽  
pp. 3425-3437 ◽  
Author(s):  
S. Bougouffa ◽  
J. K. Yang ◽  
O. O. Lee ◽  
Y. Wang ◽  
Z. Batang ◽  
...  
Keyword(s):  
Deep Sea ◽  
Sea Water ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Populations ◽  
Content Type ◽  
Deep Sea Water ◽  
Cell Counts ◽  
Red Sea Rift ◽  
Group I

ABSTRACTAtlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from theAlphaproteobacteria-dominated deep sea to thePlanctomycetaceae- orDeferribacteres-dominated interfaces to theGammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.

scholarly journals Normalization of the microbiota in patients after treatment for colonic lesions

2017 ◽  
Author(s):  
Marc A Sze ◽  
Nielson T Baxter ◽  
Mack T Ruffin ◽  
Mary AM Rogers ◽  
Patrick D Schloss
Keyword(s):  
Random Forest ◽  
Learning Algorithm ◽  
Post Treatment ◽  
16S Rrna Genes ◽  
Response To Treatment ◽  
Rrna Genes ◽  
Advanced Adenoma ◽  
P Value ◽  
Normal Colon ◽  
Bacterial Populations

AbstractBackgroundColorectal cancer is a worldwide health problem. Despite growing evidence that members of the gut microbiota can drive tumorigenesis, little is known about what happens to it after treatment for an adenoma or carcinoma. This study tested the hypothesis that treatment for adenoma or carcinoma alters the abundance of bacterial populations associated with disease to those associated with a normal colon. We tested this hypothesis by sequencing the 16S rRNA genes in the feces of 67 individuals before and after treatment for adenoma (N = 22), advanced adenoma (N = 19), and carcinoma (N = 26).ResultsThere were small changes to the bacterial community associated with adenoma or advanced adenoma and large changes associated with carcinoma. The communities from patients with carcinomas changed significantly more than those with adenoma following treatment (P-value < 0.001). Although treatment was associated with intrapersonal changes, the change in the abundance of individual OTUs in response to treatment was not consistent within diagnosis groups (P-value > 0.05). Because the distribution of OTUs across patients and diagnosis groups was irregular, we used the Random Forest machine learning algorithm to identify groups of OTUs that could be used to classify pre and post-treatment samples for each of the diagnosis groups. Although the adenoma and carcinoma models could reliably differentiate between the pre and post-treatment samples (P-value < 0.001), the advanced-adenoma model could not (P-value = 0.61). Furthermore, there was little overlap between the OTUs that were indicative of each treatment. To determine whether individuals who underwent treatment were more likely to have OTUs associated with normal colons we used a larger cohort that contained individuals with normal colons and those with adenomas, advanced adenomas, and carcinomas. We again built Random Forest models and measured the change in the positive probability of having one of the three diagnoses to assess whether the post-treatment samples received the same classification as the pre-treatment samples.Samples from patients who had carcinomas changed towards a microbial milieu that resembles the normal colon after treatment (P-value < 0.001). Finally, we were unable to detect any significant differences in the microbiota of individuals treated with surgery alone and those treated with chemotherapy or chemotherapy and radiation (P-value > 0.05).ConclusionsBy better understanding the response of the microbiota to treatment for adenomas and carcinomas, it is likely that biomarkers will eventually be validated that can be used to quantify the risk of recurrence and the likelihood of survival. Although it was difficult to identify significant differences between pre and post-treatment samples from patients with adenoma and advanced adenoma, this was not the case for carcinomas. Not only were there large changes in pre versus post-treatment samples for those with carcinoma, but these changes were towards a more normal microbiota.

scholarly journals Characterization of an Autotrophic Nitrogen-Removing Biofilm from a Highly Loaded Lab-Scale Rotating Biological Contactor

2003 ◽  
Vol 69 (6) ◽  
pp. 3626-3635 ◽  
Author(s):  
Kris Pynaert ◽  
Barth F. Smets ◽  
Stijn Wyffels ◽  
Daan Beheydt ◽  
Steven D. Siciliano ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Spatial Organization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Confocal Scanning Laser Microscopy ◽  
Surface Load ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonium Oxidation ◽  
Rotating Biological Contactor ◽  
N Removal

ABSTRACT In this study, a lab-scale rotating biological contactor (RBC) treating a synthetic NH4 + wastewater devoid of organic carbon and showing high N losses was examined for several important physiological and microbial characteristics. The RBC biofilm removed 89% � 5% of the influent N at the highest surface load of approximately 8.3 g of N m−2 day−1, with N2 as the main end product. In batch tests, the RBC biomass showed good aerobic and anoxic ammonium oxidation (147.8 � 7.6 and 76.5 � 6.4 mg of NH4 +-N g of volatile suspended solids [VSS]−1 day−1, respectively) and almost no nitrite oxidation (< 1 mg of N g of VSS−1 day−1). The diversity of aerobic ammonia-oxidizing bacteria (AAOB) and planctomycetes in the biofilm was characterized by cloning and sequencing of PCR-amplified partial 16S rRNA genes. Phylogenetic analysis of the clones revealed that the AAOB community was fairly homogeneous and was dominated by Nitrosomonas-like species. Close relatives of the known anaerobic ammonia-oxidizing bacterium (AnAOB) Kuenenia stuttgartiensis dominated the planctomycete community and were most probably responsible for anoxic ammonium oxidation in the RBC. Use of a less specific planctomycete primer set, not amplifying the AnAOB, showed a high diversity among other planctomycetes, with representatives of all known groups present in the biofilm. The spatial organization of the biofilm was characterized using fluorescence in situ hybridization (FISH) with confocal scanning laser microscopy (CSLM). The latter showed that AAOB occurred side by side with putative AnAOB (cells hybridizing with probe PLA46 and AMX820/KST1275) throughout the biofilm, while other planctomycetes hybridizing with probe PLA886 (not detecting the known AnAOB) were present as very conspicuous spherical structures. This study reveals that long-term operation of a lab-scale RBC on a synthetic NH4 + wastewater devoid of organic carbon yields a stable biofilm in which two bacterial groups, thought to be jointly responsible for the high autotrophic N removal, occur side by side throughout the biofilm.

scholarly journals Vertical variation in Vibrio community composition in Sansha Yongle Blue Hole and its ability to degrade macromolecules

2019 ◽  
Vol 2 (1) ◽  
pp. 60-72 ◽  
Author(s):  
Bei Li ◽  
Jiwen Liu ◽  
Shun Zhou ◽  
Liang Fu ◽  
Peng Yao ◽  
...  
Keyword(s):  
Organic Carbon ◽  
16S Rrna ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Tween 20 ◽  
Rrna Gene ◽  
Free Living ◽  
Blue Hole ◽  
Gene Copies

Abstract With the advantages of wide distribution, fast growth, and broad metabolic spectrum to organic carbon compounds, Vibrio may play an important role in organic carbon cycling. However, the ecological roles of Vibrio in many marine environments have not been explored. Here, the world’s deepest ‘blue hole’, the Sansha Yongle Blue Hole (SYBH) in the South China Sea, which is a geographically semi-enclosed environment featuring unique chemical characters, was investigated. The abundance, diversity and carbon source utilization capability of Vibrio were studied by quantification and high-throughput sequencing of Vibrio specific 16S rRNA genes and cultivation methods. The abundance of Vibrio in water column of the SYBH ranged from 3.78 × 104 to 7.35 × 106 16S rRNA gene copies L−1. Free-living Vibrio was more abundant than particle-associated Vibrio (~ 1.20 × 106 versus~ 2.68 × 105 gene copies L−1), indicating that Vibrio prefers a free-living life style. The Vibrio assemblages showed clear vertical stratification and could be divided into three groups: aerobic-transition, middle anaerobic and bottom anaerobic zones. Dissolved oxygen (DO), temperature, pH and salinity were the main environmental factors affecting the abundance and community composition. Cultivated Vibrio demonstrated a degrading capability to various macromolecular substrates, including starch, Tween 20/40/80, DNA, gelatin, alginate, casein, chitin, lecithin, κ-carrageenan, mannan, xylan and hyaluronic acid. This suggests that Vibrio could produce a variety of highly active extracellular enzymes. Our study provides new insights into the distribution pattern and possible role in carbon cycle of Vibrio in the unique environment of a ‘blue hole’.

scholarly journals Dynamics of a Pig Slurry Microbial Community during Anaerobic Storage and Management

2006 ◽  
Vol 72 (5) ◽  
pp. 3578-3585 ◽  
Author(s):  
Pascal Peu ◽  
Hubert Brug�re ◽  
Anne-Marie Pourcher ◽  
Monique K�rour�dan ◽  
Jean-Jacques Godon ◽  
...  
Keyword(s):  
Microbial Community ◽  
Archaeal Community ◽  
Single Strand Conformation Polymorphism ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Pig Slurry ◽  
Bacterial Populations ◽  
Cultural Methods ◽  
Total Dna ◽  
Anaerobic Storage

ABSTRACT The microbial community of a pig slurry on a farm was monitored for 6 months using both molecular and cultural approaches. Sampling was carried out at all the different stages of effluent handling, from the rearing build-up to slurry spreading. Total DNA of each sample was extracted and analyzed by PCR-single-strand conformation polymorphism (SSCP) analysis using primers targeting the 16S rRNA genes from the archaeal and bacterial domains and also the Eubacterium-Clostridium, Bacillus-Streptococcus-Lactobacillus, and Bacteroides-Prevotella groups. A comparison of the SSCP profiles showed that there were rapid changes in the dominant bacterial community during the first 2 weeks of anaerobic storage and that the community was relatively stable thereafter. Several bacterial populations, identified as populations closely related to uncultured Clostridium and Porphyromonas and to Lactobacillus and Streptococcus cultured species commonly isolated from pig feces, remained present and dominant from the rearing build-up to the time of spreading. Enumeration of fecal indicators (enterococci and Escherichia coli) performed in parallel using cultural methods revealed the same trends. On the other hand, the archaeal community adapted slowly during pig slurry storage, and its diversity increased. A shift between two hydrogenotrophic methanogenic Methanobrevibacter populations from the storage pit to the pond was observed. Microorganisms present in pig slurry at the time of spreading could not be detected in soil after spreading by either molecular or cultural techniques, probably because of the detection limit inherent in the two techniques.

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