Community structure of bacterioplankton and its relationship with environmental factors in the upper reaches of the Heihe River in Qinghai Plateau.

Planktonic microorganisms play a key role in the biogeochemical processes of the aquatic system, and they may be affected by many factors. High-throughput sequencing technology was used in this study to investigate and study the bacterioplankton community of water bodies in the upper reaches of the Heihe River Basin in Qinghai Plateau. Results showed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria are the predominant phyla in this river section, while the main genera are Thiomonas, Acidibacillus, Acidocella, Rhodanobacter, Acidithiobacter and Gallionella, which are autochthonous in the acid-mine drainage. Additionally, total nitrogen, total phosphorus, permanganate index and pH are significantly correlated with the bacterioplankton abundance and are the main limiting factors for the spatial distribution of the bacterioplankton. PICRUSt inferred that the mainstream microbial assemblages had a higher abundance of KOs belong to metabolism of terpenoids and polyketides, while the tributary had higher abundance of KOs belong to the immune system. The relationship between bacterioplankton community composition and environmental factors in the Heihe River basin was discussed for the first time in this study, which provides a theoretical basis for the healthy, orderly development of the water environment in the Heihe River Basin.

Changes in microbial community in the presence of oil and chemical dispersant and their effects on the corrosion of API 5L steel coupons in a marine-simulated microcosm.

The influence of crude oil and chemical dispersant was evaluated over planktonic bacteria and biofilms grown on API 5L steel surfaces in microcosm systems. Three conditions were simulated, an untreated marine environment and a marine environment with the presence of crude oil and a containing crude oil and chemical dispersant. The results of coupon corrosion rates indicated that in the oil microcosm, there was a high corrosion rate when compared with the other two systems. Analysis of bacterial communities by 16S rRNA gene sequencing described a clear difference between the different treatments. In plankton communities, the Bacilli and Gammaproteobacteria classes were the most present in numbers of operational taxonomic unit (OTUs). The Vibrionales, Oceanospirillales, and Alteromonadales orders were predominant in the treatment with crude oil, whereas in the microcosm containing oil and chemical dispersant, mainly members of Bacillales order were detected. In the communities analyzed from biofilms attached to the coupons, the most preponderant class was Alphaproteobacteria, followed by Gammaproteobacteria. In the control microcosm, there was a prevalence of the orders Rhodobacterales, Aeromonadales, and Alteromonadales, whereas in the dispersed oil and oil systems, the members of the order Rhodobacterales were present in a larger number of OTUs. These results demonstrate how the presence of a chemical dispersant and oil influence the corrosion rate and bacterial community structures present in the water column and biofilms grown on API 5L steel surfaces in a marine environment. KEY POINTS: • Evaluation of the effects of oil and chemical surfactants on the corrosion of API 5L. • Changes in microbial communities do not present corrosive biofilm on API 5L coupons.

Plankton crustaceans in bays with different trophic status in Llanquihue lake (41° S Chile) / Crustáceos planctónicos crustáceo em baías com estado trófico diferente no lago Llanquihue (41° S Chile)

Abstract The Llanquihue lake is included in the called Araucanian or Nord Patagonian lakes located between 38-41° S. These lakes are characterized by their oligo-mesotrophic status due to human intervention which takes to the increase in nutrients inputs from industries and towns. Effects on zooplankton assemblages are observed with marked increase of daphnids abundance. The aim of the present study is to analyze the trophic status and zooplankton relative abundance in different bays of Llanquihue lake. It was found direct associations between chlorophyll a with daphnids percentage, total dissolved nitrogen with reactive soluble phosphorus nitrogen/phosphorus molar radio with cyclopoids percentage, and an inverse relation between daphnids and calanoids percentages. The occurrence of three kinds of microcrustacean assemblages and environmental conditions was evidenced: the first one with high calanoids percentage, low species number and low chlorophyll and nutrients concentration, a second with moderate chlorophyll and nutrients concentration and moderate daphnids percentage; high species number and a third site with high chlorophyll and nutrients concentration, high daphnids percentage and high species number. Daphnids increase under mesotrophic status, agree with similar results observed for southern Argentinean and New Zealand lakes.

Resumo O lago Llanquihue está incluído nos chamados lagos araucana ou Nord Patagônia localizado entre 38-41° S. Estes lagos são caracterizados pela condicao oligo-mesotrofica debido a intervencao humana, com aumento da carga de nutrientes provenientes de industrias y areas urbanas com efeitos sobre as assembleias zooplantonicas sao observadas, com aumento acentuado de dafnideos. O objetivo do presente estudo é analisar o estado trófico a abundancia relative do zooplancton em diferentes compartimentos do lago Llanquihue. Foram encontradas associações diretas entre clorofila a com percentual de dafinídeos, nitrogênio total dissolvido com fósforo solúvel reativo molares razao molar nitrogênio / fósforo com percentual de ciclopóides, e uma relação inversa entre percentuais de dafinídeos e calanóides porcentagens. A ocorrência de três tipos de assembleias de microcrustáceos e as condições ambientais fora: a primeira com alta porcentais de calanóides, baixo número de espécies e baixa clorofila e a nutrientes, uma segunda com concentracoes moderadas de clorofila e nutrientes percentual moderado de daphnideos e alto número de espécies; e uma terceiro local com alta concentração de clorofila e nutrientes, alta abundância dafinídeos e número elevado de espécies. Resultados similares com aumento de dafnideos em condicoes mesotroficas também foram observados para lagos da Argentina e Nova Zelândia do sul.

Plankton crustaceans in bays with different trophic status in Llanquihue lake (41° S Chile).

The Llanquihue lake is included in the called Araucanian or Nord Patagonian lakes located between 38-41° S. These lakes are characterized by their oligo-mesotrophic status due to human intervention which takes to the increase in nutrients inputs from industries and towns. Effects on zooplankton assemblages are observed with marked increase of daphnids abundance. The aim of the present study is to analyze the trophic status and zooplankton relative abundance in different bays of Llanquihue lake. It was found direct associations between chlorophyll a with daphnids percentage, total dissolved nitrogen with reactive soluble phosphorus nitrogen/phosphorus molar radio with cyclopoids percentage, and an inverse relation between daphnids and calanoids percentages. The occurrence of three kinds of microcrustacean assemblages and environmental conditions was evidenced: the first one with high calanoids percentage, low species number and low chlorophyll and nutrients concentration, a second with moderate chlorophyll and nutrients concentration and moderate daphnids percentage; high species number and a third site with high chlorophyll and nutrients concentration, high daphnids percentage and high species number. Daphnids increase under mesotrophic status, agree with similar results observed for southern Argentinean and New Zealand lakes.

Variables influencing extraction of nucleic acids from microbial plankton (viruses, bacteria, and protists) collected on nanoporous aluminum oxide filters.

Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not been systematically or quantitatively evaluated. In this study, we characterized the flux of water through commercially produced nanoporous (0.02 µm) AAO filters (Anotop; Whatman) and used isolates (a virus, a bacterium, and a protist) and natural seawater samples to test variables that we expected would influence the efficiency with which nucleic acids are recovered from the filters. Extraction chemistry had a significant effect on DNA yield, and back flushing the filters during extraction was found to improve yields of high-molecular-weight DNA. Using the back-flush protocol, the mass of DNA recovered from microorganisms collected on AAO filters was ≥ 100% of that extracted from pellets of cells and viruses and 94% ± 9% of that obtained by direct extraction of a liquid bacterial culture. The latter is a minimum estimate of the relative recovery of microbial DNA, since liquid cultures include dissolved nucleic acids that are retained inefficiently by the filter. In conclusion, we demonstrate that nucleic acids can be extracted from microorganisms on AAO filters with an efficiency similar to that achievable by direct extraction of microbes in suspension or in pellets. These filters are therefore a convenient means by which to harvest total microbial communities from multiple aqueous samples in parallel for subsequent molecular analyses.

Rapid coupling between ice volume and polar temperature over the past 150,000 years.

Current global warming necessitates a detailed understanding of the relationships between climate and global ice volume. Highly resolved and continuous sea-level records are essential for quantifying ice-volume changes. However, an unbiased study of the timing of past ice-volume changes, relative to polar climate change, has so far been impossible because available sea-level records either were dated by using orbital tuning or ice-core timescales, or were discontinuous in time. Here we present an independent dating of a continuous, high-resolution sea-level record in millennial-scale detail throughout the past 150,000 years. We find that the timing of ice-volume fluctuations agrees well with that of variations in Antarctic climate and especially Greenland climate. Amplitudes of ice-volume fluctuations more closely match Antarctic (rather than Greenland) climate changes. Polar climate and ice-volume changes, and their rates of change, are found to covary within centennial response times. Finally, rates of sea-level rise reached at least 1.2 m per century during all major episodes of ice-volume reduction.

Marine bacterial, archaeal and protistan association networks reveal ecological linkages.

Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico-chemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible 'keystone' species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes.

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.

Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.

Applying a most probable number method for enumerating planktonic, dissimilatory, ammonium-producing, nitrate-reducing bacteria in oil field waters.

A most probable number (MPN) method was used to enumerate dissimilatory ammonium-producing, nitrate-reducing bacteria (DAP-NRB) in oil field waters and to determine whether they were stimulated by nitrate addition used to control hydrogen sulfide production. An ammonium production medium with 5 carbon and energy sources (acetate, glucose, glycerol, pyruvate, and succinate) and nitrate was used in a 3-tube MPN procedure to enumerate DAP-NRB. These bacteria were detected in 12 of 18 oil field water samples, but they were seldom detected in wellhead samples. Three oil field water samples were amended with nitrate in serum bottles and the numbers of different NRB were determined over a 38-day incubation time. This amendment stimulated increases in the numbers of heterotrophic NRB and autotrophic nitrate-reducing, sulfide-oxidizing bacteria, but DAP-NRB remained a minor portion of these communities. Overall, DAP-NRB were present in many of the oil field waters that were examined but their numbers were low. It appears that DAP-NRB would play a minor role in the consumption of nitrate injected into oil field waters for the control of hydrogen sulfide production.

Influence of top-down and bottom-up manipulations on the R-BT065 subcluster of beta-proteobacteria, an abundant group in bacterioplankton of a freshwater reservoir.

We studied the effects of nutrient availability and protistan grazing on bacterial dynamics and community composition (BCC) in different parts of the canyon-shaped Rímov reservoir (Czech Republic). The effects of protistan grazing on BCC were examined using a size fractionation approach. Water from the dam area with only bacteria (<0.8 microm), bacteria and heterotrophic nanoflagellates (<5 microm), or whole water were incubated in situ inside dialysis bags. Top-down or predator manipulations (size fractionation) were also combined with bottom-up or resource manipulations, i.e., transplantation of samples to the middle and upper inflow parts of the reservoir with increased phosphorus availability. Significant genotypic shifts in BCC occurred with transplantation as indicated by denaturing gradient gel electrophoresis. Using different probes for fluorescence in situ hybridization, we found that 10 to 50% of total bacteria were members of the phylogenetically small cluster of beta-proteobacteria (targeted with the probe R-BT065). These rod-shaped cells of very uniform size were vulnerable to predation but very fast growing and responded markedly to the different experimental manipulations. In all the grazer-free treatments, the members of the R-BT065 cluster showed the highest net growth rates of all studied bacterial groups. Moreover, their relative abundance was highly correlated with bacterial bulk parameters and proportions of bacteria with high nucleic acid (HNA) content. In contrast, increasing protistan bacterivory yielded lower proportions of R-BT065-positive and HNA bacteria substituted by increasing proportions of the class Actinobacteria, which profited from the enhanced protistan bacterivory.