Nitrous Oxide Emission from Full-Scale Anammox-Driven Wastewater Treatment Systems.

Wastewater treatment plants (WWTPs) are important contributors to global greenhouse gas (GHG) emissions, partly due to their huge emission of nitrous oxide (N2O), which has a global warming potential of 298 CO2 equivalents. Anaerobic ammonium-oxidizing (anammox) bacteria provide a shortcut in the nitrogen removal pathway by directly transforming ammonium and nitrite to nitrogen gas (N2). Due to its energy efficiency, the anammox-driven treatment has been applied worldwide for the removal of inorganic nitrogen from ammonium-rich wastewater. Although direct evidence of the metabolic production of N2O by anammox bacteria is lacking, the microorganisms coexisting in anammox-driven WWTPs could produce a considerable amount of N2O and hence affect the sustainability of wastewater treatment. Thus, N2O emission is still one of the downsides of anammox-driven wastewater treatment, and efforts are required to understand the mechanisms of N2O emission from anammox-driven WWTPs using different nitrogen removal strategies and develop effective mitigation strategies. Here, three main N2O production processes, namely, hydroxylamine oxidation, nitrifier denitrification, and heterotrophic denitrification, and the unique N2O consumption process termed nosZ-dominated N2O degradation, occurring in anammox-driven wastewater treatment systems, are summarized and discussed. The key factors influencing N2O emission and mitigation strategies are discussed in detail, and areas in which further research is urgently required are identified.

Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe.

Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.

Salinity Drives Functional and Taxonomic Diversities in Global Water Metagenomes.

A tight association between microbial function and taxonomy is the basis of functional prediction based on taxonomy, but such associations have been controversial in water biomes largely due to the probable prevalence of functional redundancy. However, previous studies on this topic used a relatively coarse resolution of ecosystem functioning, potentially inflating the estimated functional redundancy. Thus, a comprehensive evaluation of the association between high-resolution functional traits and taxonomic diversity obtained from fresh and saline water metagenomic data is urgently needed. Here, we examined 938 functionally and taxonomically annotated water metagenomes obtained worldwide to scrutinize the connection between function and taxonomy, and to identify the key driver of water metagenomes function or taxonomic composition at a global scale. We found that pairwise similarity of function was significantly associated with taxonomy, though taxonomy had higher global dissimilarity than function. Classification into six water biomes resulted in greater variation in taxonomic compositions than functional profiles, as the key regulating factor was salinity. Fresh water microbes harbored distinct functional and taxonomic structures from microbes in saline water biomes, despite that taxonomy was more susceptible to gradient of geography and climate than function. In summary, our results find a significant relationship between taxonomic diversity and microbial functioning in global water metagenomes, although microbial taxonomic compositions vary to a larger extent than functional profiles in aquatic ecosystems, suggesting the possibility and necessity for functional prediction of microorganisms based on taxonomy in global aquatic ecosystems.

Stable Soil Microbial Functional Structure Responding to Biodiversity Loss Based on Metagenomic Evidences.

Anthropogenic disturbances and global climate change are causing large-scale biodiversity loss and threatening ecosystem functions. However, due to the lack of knowledge on microbial species loss, our understanding on how functional profiles of soil microbes respond to diversity decline is still limited. Here, we evaluated the biotic homogenization of global soil metagenomic data to examine whether microbial functional structure is resilient to significant diversity reduction. Our results showed that although biodiversity loss caused a decrease in taxonomic species by 72%, the changes in the relative abundance of diverse functional categories were limited. The stability of functional structures associated with microbial species richness decline in terrestrial systems suggests a decoupling of taxonomy and function. The changes in functional profile with biodiversity loss were function-specific, with broad-scale metabolism functions decreasing and typical nutrient-cycling functions increasing. Our results imply high levels of microbial physiological versatility in the face of significant biodiversity decline, which, however, does not necessarily mean that a loss in total functional abundance, such as microbial activity, can be overlooked in the background of unprecedented species extinction.

Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae).

Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.

Evaluation of a multimodality MR/US coregistration system for investigation of hepatic metastases from colorectal cancer.

PURPOSE: To evaluate a magnetic resonance (MR)/ultrasound (US) coregistration system with US used in follow-up diagnostic studies of lesions originally identified by MR imaging. MATERIALS AND METHODS: A single-center prospective study enrolled 21 consecutive patients (age, 64.0 y±7.5; eight men [age, 63.0 y±7.1] and 13 women [age, 65.0 y±7.3]) evaluated for potential surgical resection of liver metastases. Each patient underwent same-day MR examination and two US examinations: one regular and one with the MR/US coregistration system. Target lesions were identified on MR imaging, and US was used in follow-up diagnostic studies of lesions originally identified by MR imaging. During US, two outcome measures (target localization success and target localization time) were collected. Ratios of lesions found per patient were compared with a paired Wilcoxon test, and a Student t test was used to compare target localization time. RESULTS: Ratios of lesions found per patient with the coregistered system (93.7%) and conventional US (73.3%) were statistically different (P =.003). Lesions found by the coregistration system but not conventional US were statistically smaller than those found by both systems (6.1 mm±4.0 vs 15.6 mm±9.8; P<.0006). There was no statistical difference in target localization time for detection of lesions found by coregistered (100 s±89) and conventional US (108 s±86; P = .78). CONCLUSIONS: The MR/US coregistration system increases the number of lesions detected with US versus standard US alone. This may prove beneficial in surgical and nonsurgical management of patients with focal liver lesions.

Pseudogene: lessons from PCR bias, identification and resurrection.

Pseudogenes are fragments of non-functional genomic DNA with high sequences similarity to normal functional genes. They are a kind of non-coding DNA produced by gene duplications or retrotranspositions. Pseudogenes exist in human genome at a large quantity which is nearly as much as that of normal functional genes. They could cause PCR bias in molecular biology experiments and confuse related analysis. On the other hand, pesudogenes are important elements in genomics study for getting an integral picture of genome annotation. They give diverse information of evolutionary history and are regarded as genome fossils. Worldwide research project "encyclopedia of DNA elements"(ENCODE) founded in recent years have enhanced our understanding of pseudogenes. Approaches established to identify pseudogenes include PseudoPipe, HAVANA method, PseudoFinder, RetroFinder, GIS-PET method and consensus method. This paper discuss pseudogenes with respect to the formation mechanisms, distribution, and problems for PCR, importance and identification of pseudogenes. Furthermore, potential resurrection of pseudogenes and their potential function are discussed.