Microbial Succession and Nitrogen Cycling in Cultured Biofilms as Affected by the Inorganic Nitrogen Availability

Biofilms play important roles in nutrients and energy cycling in aquatic ecosystems. We hypothesized that as eutrophication could change phytoplankton community and decrease phytoplankton diversity, ambient inorganic nitrogen level will affect the microbial community and diversity of biofilms and the roles of biofilms in nutrient cycling. Biofilms were cultured using a flow incubator either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def). The results showed that the biomass and nitrogen and phosphorous accumulation of biofilms were limited by N deficiency; however, as expected, the N-def biofilms had significantly higher microbial diversity than that of N-rep biofilms. The microbial community of biofilms shifted in composition and abundance in response to ambient inorganic nitrogen level. For example, as compared between the N-def and the N-rep biofilms, the former consisted of more diazotrophs, while the latter consisted of more denitrifying bacteria. As a result of the shift of the functional microbial community, the N concentration of N-rep medium kept decreasing, while that of N-def medium showed an increasing trend in the late stage. This indicates that biofilms can serve as the source or the sink of nitrogen in aquatic ecosystems, and it depends on the inorganic nitrogen availability.</p

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Precipitation mediate the distribution of phytoplankton communities in a tributary of Three Gorges Reservoir

Abstract Precipitation is a driver of changes in spatiotemporal distribution of phytoplankton communities. The ecological consequences of precipitation is importance but the underlying processes are not clear. Here we conducted an immediate prior- and after-event short-interval investigation in the Three Gorges Reservoir region, to test whether the short-term changes in the phytoplankton communities and functional groups could be predicted based on the precipitation level. We found that precipitation of moderate and high levels immediately changed the phytoplankton distribution and altered functional groups. According to structural equation model, the vertical velocity (λ = -0.81), Zeu/Zmix (λ = 0.47) and RWCS (λ = 0.38) were important parameters for phytoplankton distribution during the precipitation event. Water quality was not directly affected phytoplankton distribution (λ = -0.11) and effects of precipitation on the water quality only lasted 1–2 days. Phytoplankton community was redistributed with some tolerance functional groups appearance, such as group F, Lo, M and groups M, MP, TB, W1 appeared during- and after- precipitation event, respectively. We also found that the mixing rather than flushing was the driving force for the decrease of phytoplankton biomass. Our study provided valuable data for reservoir regulation and evidence for predictions of phytoplankton during the precipitation events under different climate change scenarios.</jats:p

Precipitation Mediates the Distribution but Not the Taxonomic Composition of Phytoplankton Communities in a Tributary of Three Gorges Reservoir

Precipitation is a driver of changes in the spatiotemporal distribution of phytoplankton communities. The ecological consequence of precipitation is important, but the underlying processes are not clear. Here we conducted an immediate prior- and after-event short-interval investigation in the Three Gorges Reservoir region, to test whether the short-term changes in the phytoplankton communities and functional groups could be predicted based on the precipitation level. We found that precipitation of moderate and high levels immediately changed the phytoplankton distribution and altered functional groups. According to structural equation model, the vertical velocity (λ = −0.81), light availability (Zeu/Zmix, λ = 0.47) and relative water column stability (RWCS, λ = 0.38) were important parameters for phytoplankton distribution during the precipitation event. Water quality did not directly affect phytoplankton distribution (λ = −0.11) and effects of precipitation on the water quality only lasted 1–2 days. The phytoplankton community was redistributed with some tolerance functional groups appearance, such as groups F, Lo, M and groups M, MP, TB, W1 appeared during- and after- precipitation event, respectively. We also found that mixing rather than flushing was the driving force for the decrease of phytoplankton biomass. Our study provided valuable data for reservoir regulation and evidence for predictions of phytoplankton during the precipitation events under different climate change scenarios.</jats:p

Regulating Nutrients and Phytoplankton by Extending the Habitats of Periphyton in a Deep River-Type Reservoir

Eutrophication and phytoplankton blooms threaten the water quality of many reservoirs, especially deep ones. Periphyton is an important component of aquatic ecosystems that can compete with phytoplankton for light and nutrients. However, studies on the dynamics of periphyton development in deep reservoirs are rare. Here, the growth characteristics of periphyton on the artificial substrate (AS) in both open water and enclosures of the Three Gorges Reservoir (TGR) are investigated. The development and relative importance of periphyton are analyzed. The results indicate that mass growth of periphyton is observed on the AS platforms after several weeks. A potential phosphorus limitation for periphyton development in the TGR is evidenced by the relatively high TN/TP ratio in the water column. The differences of phytoplankton biomass in two enclosures suggest the existence of interactions between phytoplankton and periphyton. The results indicate that the artificially loaded AS on the water surface of the deep reservoir leads to the redistribution of nutrients and light between phytoplankton and periphyton. The results are very encouraging because the use of AS for periphyton incubation is an economical and practical way to reduce the probability of phytoplankton blooms in deep reservoirs, especially when the nutrient loads cannot be reduced effectively in a short period