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The Taitung region is one of Taiwan’s main places for ginger agriculture. Due to issues with disease and nutrient, farmers cannot use continuous cropping techniques on ginger, meaning that the ginger industry is constantly searching for new lands. Continuous cropping increases the risk of infection by Pythium myriotylum and Ralstonia solanacearum, which cause soft rot disease and bacterial wilt, respectively. In addition, fertilizer additives cannot recover the soil when using continuous cropping on ginger, even when there is no decrease in trace elements observed in the soil. Although there may be other reasons for the reduction in production, such as soil microbes, we know little about the soil microbiome associated with ginger cultivation. Hence, in this study, we used the bacterial 16S V3–V4 hypervariable region of the 16S ribosomal RNA region to investigate microbe compositions in ginger soil to identify the difference between ginger soil with and without disease. Later, to investigate the influence of the well-known biocontrol agent-B. velezensis and fungicide Etridiazole on soil microbes and ginger productivity, we designed an experiment that collected the soil samples according to the different ginger cultivation periods to examine the microbial community dynamics in the rhizome and bulk soil. We demonstrated that B. velezensis is beneficial to ginger reproduction and suggest that it may influence the plant by adjusting its soil microbial composition. Etridiazole, on the other hand, may have some side effects on the ginger or beneficial bacteria in the soils, inhibiting ginger reproduction.

Background and Aims Patients with end-stage kidney disease (ESKD) are characterized by altered gut microbiota, impaired intestinal barrier function, and experienced gut microbiota-derived metabolites related to systemic complications. However, limited studies evaluated the microbial diversity and function in ESKD patients previously. Method Compared to age- and gender-matched subjects without kidney disease, 82 ESKD patients in the discovery cohort and 58 ESKD patients in the validation cohort were investigated for the microbial richness, biodiversity, gut dysbiosis, microbial composition differences, and the functional changes by gut metabolic module analysis. Bacterial derived free form protein-bound uremic toxins were analyzed by mass spectrometry and their association with microbial richness in ESKD patients was determined. Results Compared to controls, an increased α-diversity and distinct β-diversity were found in ESKD (Figure). The increase in α-diversity was correlated with protein-bound uremic toxins, particularly hippuric acid. A higher microbial dysbiosis index (MDI) was found in ESKD patients with the following enriched genera: Facealibacterium, Ruminococcus, Fusobacterium, Dorea, Anaerovorax, Sarcina, Akkermansia, Streptococcus, and Dysgonomonas. MDI at the genus level successfully differentiated between ESKD and controls in the discovery cohort (area under the curve [AUC] of 81.9%) and the validation cohort (AUC of 83.2%). Regarding functional enrichment analysis with gut metabolic modules, ESKD subjects presented with gut microbial function of increased saccharide and amino acid metabolism compared with matched controls. Conclusion An enriched but dysbiotic gut microbiota was presented in ESKD patients, in which the bacteria that were present increase amino acid metabolism linked to the production of protein-bound uremic toxins.

Background: Patients with end-stage renal disease (ESRD) have extremely high risks of mortality and morbidity, as well as altered gut microbiota and impaired intestinal barrier function. The translocation of gut-derived molecules in ESRD contributes to systemic complications. In this study, we evaluated the gut microbiome difference in ESRD patients compared to age- and gender-matched subjects without kidney disease in discovery and validation cohorts.Results: Compared to controls with normal renal function, an increased α-diversity and distinct β-diversity were found in ESRD subjects. The increase in α-diversity was correlated with protein-bound uremic toxins, particularly hippuric acid. A higher microbial dysbiosis index (MDI) was found in ESRD patients with the following enriched genera: Facealibacterium, Ruminococcus, Fusobacterium, Dorea, Anaerovorax, Sarcina, Akkemansia, Streptococcus, and Dysgonomonas. MDI at the genus level demonstrated highly differentiated accuracies between ESRD and control subjects in the discovery cohort (area under the curve [AUC] of 81.9%) and between ESRD and control subjects in the validation cohort (AUC of 83.2%). On functional enrichment analysis with gut metabolic modules, ESRD subjects presented with increased saccharide and amino acid metabolism when compared with matched controls.Conclusions: An enriched but dysbiotic gut microbiota was presented in ESRD patients, in which the bacteria that were present increase amino acid metabolism linked to the production of protein-bound uremic toxins.

Objectives: A question central to the Covid-19 pandemic is why the Covid-19 mortality rate varies so greatly across countries. This study aims to investigate factors associated with cross-country variation in Covid-19 mortality.Methods: Covid-19 mortality rate was calculated as number of deaths per 100 Covid-19 cases. To identify factors associated with Covid-19 mortality rate, a multivariable linear regression model was applied to a cross-sectional dataset comprising 78 countries and 1,790,550 patients infected by Covid-19. We retrieved data from the Worldometer website and the Worldwide Governance Indicators and World Development Indicators databases.Results: Covid-19 mortality rate was negatively associated with Covid-19 test number per 1,000 population (RR=0.97; 95% CI 0.96 to 0.99, P=0.013) and government effectiveness indicator (RR=0.96; 95% CI 0.93 to 0.98, P=0.001). Covid-19 mortality rate was positively associated with number of critical cases per 100 Covid-19 cases, Covid-19 case number per 10,000 population, proportion of population aged 65 or older and proportion of deaths attributable to communicable diseases in previous years (all with PConclusions: Multiple factors were associated with Covid-19 mortality rates. Increasing Covid-19 testing and improving government effectiveness may have the potential to attenuate Covid-19 mortality.Authors Li-Lin Liang and Chun-Ying Wu contributed equally to this work.

Objectives The intestinal microbiota has been known to involve in obesity and host immune response. We aimed to investigate the intestinal microbiota and potential genetic function in relation to clinical presentation in psoriasis patients. Methods Faecal microbiota and predicted genetic function inferred from high-throughput 16S ribosomal RNA sequencing were analysed between psoriasis (n = 32) and age-, gender- and body mass index (BMI)-matched non-psoriasis subjects (n = 64), from a referral medical centre. The correlation between altered microbiota and disease activity, arthritis and systemic anti-psoriatic drugs was also investigated. Results We observed a distinct faecal microbial community structure in psoriasis patients, with an increased abundance of phylum Firmicutes and decreased abundance of phylum Bacteroidetes, across different subgroup of subjects. Ruminococcus and Megasphaera, of the phylum Firmicutes, were the top-two genera of discriminant abundance in psoriasis. A number of functional genes and metabolic pathways involving bacterial chemotaxis and carbohydrate transport were predicted over-represented, whereas genes related to cobalamin and iron transport were predicted under-represented in faecal microbiota of psoriasis patients. Conclusions The distinct faecal microbial composition in psoriasis might be associated with altered transport of carbohydrate, cobalamin and iron, as well as chemotaxis.

Endozoicomonas bacteria are commonly regarded as having a potentially symbiotic relationship with their coral hosts. However, their diversity and phylogeny in samples collected from various sources remain unclear. Therefore, we designed an Endozoicomonas-specific primer paired with a bacterial universal primer to detect the 16S ribosomal RNA (rRNA) genes of this taxon and conducted an in-depth investigation of the Endozoicomonas community structure in reef-building corals. The primer had high specificity in the V3-V4 region (95.6%) and its sensitivity was high, particularly when Endozoicomonas was rare in samples (e.g., in seawater, which had a higher alpha diversity of Endozoicomonas than corals). In coral samples, predominant V3-V4 ribotypes had greater divergence than predominant V1-V2 ribotypes, and were grouped into at least 9 novel clades in a phylogenetic tree, indicating Endozoicomonas had high phylogenetic diversity. Divergence within this genus was potentially higher than that among 7 outgroup genera based on the phylogenetic distances of partial 16S rDNA sequences, suggesting that the taxonomy of this genus needs to be revised. In conclusion, dominant Endozoicomonas populations had variable phylogenies; furthermore, the newly designed primers may be useful molecular tools for the reliable detection of the Endozoicomonas community in marine environments.

Microbial endoliths, which inhabit interior pores of rocks, skeletons and coral, are ubiquitous in terrestrial and marine environments. In this study, various colored layers stratified the endolithic environment within the skeleton of Isopora palifera; however, there was a distinct green-pigmented layer in the skeleton (beneath the living coral tissue). To characterize diversity of endolithic microorganisms, 16S ribosomal RNA gene amplicon pyrosequencing was used to investigate bacterial communities in the green layer of eight I. palifera coral colonies retrieved from two locations on Green Island, Taiwan. The dominant bacterial group in the green layer belonged to the bacterial phylum Chlorobi, green sulfur bacteria capable of anoxygenic photosynthesis and nitrogen fixation. Specifically, bacteria of the genus Prosthecochloris were dominant in this green layer. To our knowledge, this is the first study to provide a detailed profile of endolithic bacteria in coral and to determine the prevalence of Prosthecochloris in the green layer. Based on our findings, we infer that these bacteria may have an important functional role in the coral holobiont in the nutrient-limited coral reef ecosystem.

Diet and exercise are conventional methods for controlling body weight and are linked to alterations in gut microbiota. However, the associations of diet, exercise, and gut microbiota in the control of obesity remain largely unknown. In the present study, using 16S rRNA amplicon sequencing and fecal microbiota transplantation (FMT), normal fat diet (NFD), exercise and their combination resulted in improved metabolic profiles in comparison to sedentary lifestyle with high fat diet (HFD). Moreover, diet exerted more influence than exercise in shaping the gut microbiota. HFD-fed mice receiving FMT from NFD-exercised donors not only showed remarkably reduced food efficacy, but also mitigated metabolic profiles (p Helicobacter, Odoribacter and AF12 and overrepresentation of oxidative phosphorylation and glycolysis genes. Our findings demonstrate that the beneficial effects of diet and exercise are transmissible via FMT, suggesting a potential therapeutic treatment for obesity.

Obesity is worldwide epidemic given its rapid growth in global prevalence. Among the risk factors contributing to obesity, human gut microbiome recently emerges with unprecedented intimacy in host metabolism and inflammation. With the advances in sequencing technology, more and more detailed understandings towards the intricate relationships linking gut microbiome and obesity have been continuously disclosed. Herein, we review studies resolving associations between gut microbiome and obesity, and then mechanistic studies tackling the roles played by gut microbes in obesogenic physiology. Keywords: Gut microbiome, Gut microbiota, Obesity

Seasonal variation in temperature fluctuations may provide corals and their algal symbionts varying abilities to acclimate to changing temperatures. We hypothesized that different temperature ranges between seasons may promote temperature-tolerance of corals, which would increase stability of a bacterial community following thermal stress. Acropora muricata coral colonies were collected in summer and winter (water temperatures were 23.4–30.2 and 12.1–23.1 °C, respectively) from the Penghu Archipelago in Taiwan, then exposed to 6 temperature treatments (10–33 °C). Changes in coral-associated bacteria were determined after 12, 24, and 48 h. Based on 16S rRNA gene amplicons and Illumina sequencing, bacterial communities differed between seasons and treatments altered the dominant bacteria. Cold stress caused slower shifts in the bacterial community in winter than in summer, whereas a more rapid shift occurred under heat stress in both seasons. Results supported our hypothesis that bacterial community composition of corals in winter are more stable in cold temperatures but changed rapidly in hot temperatures, with opposite results for the bacterial communities in summer. We infer that the thermal tolerance ranges of coral-associated bacteria, with a stable community composition, are associated with their short-term (3 mo) seawater thermal history. Therefore, seasonal acclimation may increase tolerance of coral-associated bacteria to temperature fluctuations.

Microbes are the most abundant biological entities on earth, therefore, studying them is important for understanding their roles in global ecology. The science of metagenomics is a relatively young field of research that has enjoyed significant effort since its inception in 1998. Studies using next-generation sequencing techniques on single genomes and collections of genomes have not only led to novel insights into microbial genomics, but also revealed a close association between environmental niches and genome evolution. Herein, we review studies investigating microbial genomics (largely in the marine ecosystem) at the individual and community levels to summarize our current understanding of microbial ecology in the environment.

Extreme climatic activities, such as typhoons, are widely known to disrupt our natural environment. In particular, studies have revealed that typhoon-induced perturbations can result in several long-term effects on various ecosystems. In this study, we have conducted a 2-year metagenomic survey to investigate the microbial and viral community dynamics associated with environmental changes and seasonal variations in an enclosed freshwater reservoir subject to episodic typhoons. We found that the microbial community structure and the associated metagenomes continuously changed, where microbial richness increased after typhoon events and decreased during winter. Among the environmental factors that influenced changes in the microbial community, precipitation was considered to be the most significant. Similarly, the viral community regularly showed higher relative abundances and diversity during summer in comparison to winter, with major variations happening in several viral families including Siphoviridae, Myoviridae, Podoviridae and Microviridae. Interestingly, we also found that the precipitation level was associated with the terrestrial viral abundance in the reservoir. In contrast to the dynamic microbial community (L-divergence 0.73 ± 0.25), we found that microbial metabolic profiles were relatively less divergent (L-divergence 0.24 ± 0.04) at the finest metabolic resolution. This study provides for the first time a glimpse at the microbial and viral community dynamics of a subtropical freshwater ecosystem, adding a comprehensive set of new knowledge to aquatic environments.

Simple, reliable, lightweight, and inexpensive thin films based sensors are still in intense development and high demand in many applications such as biomedical, industrial, environmental, military, and consumer products. One important class of sensors is the optical pH sensor. In addition, conformal thin film based sensors extend the range of application for pH optical sensors. We present the results on the fabrication and characterization of optical pH sensing coatings made through ionic self-assembled technique. These thin films are based on the combination of a polyelectrolyte and water-soluble organic dye molecule Direct Yellow 4. A series of films was fabricated and characterized in order to determine the optimized parameters of the polymer and of the organic dye solutions. The optical pH responses of these films were also studied. The transparent films were immersed in solutions at various temperature and pH values. The films are stable when immersed in solutions with pH below 9.0 and temperatures below 90 °C and they maintain their performance after longer immersion times. We also demonstrate the functionality of these coatings as conformal films.

Subtotal gastrectomy (i.e., partial removal of the stomach), a surgical treatment for early-stage distal gastric cancer, is usually accompanied by highly selective vagotomy and Billroth II reconstruction, leading to dramatic changes in the gastric environment. Based on accumulating evidence of a strong link between human gut microbiota and host health, a 2-year follow-up study was conducted to characterize the effects of subtotal gastrectomy. Gastric microbiota and predicted gene functions inferred from 16S rRNA gene sequencing were analyzed before and after surgery. The results demonstrated that gastric microbiota is significantly more diverse after surgery. Ralstonia and Helicobacter were the top two genera of discriminant abundance in the cancerous stomach before surgery, while Streptococcus and Prevotella were the two most abundant genera after tumor excision. Furthermore, N-nitrosation genes were prevalent before surgery, whereas bile salt hydrolase, NO and N2O reductase were prevalent afterward. To our knowledge, this is the first report to document changes in gastric microbiota before and after surgical treatment of stomach cancer.

Terrestrial mud volcanism represents the prominent surface geological feature, where fluids and hydrocarbons are discharged along deeply rooted structures in tectonically active regimes. Terrestrial mud volcanoes (MVs) directly emit the major gas phase, methane, into the atmosphere, making them important sources of greenhouse gases over geological time. Quantification of methane emission would require detailed insights into the capacity and efficiency of microbial metabolisms either consuming or producing methane in the subsurface, and establishment of the linkage between these methane-related metabolisms and other microbial or abiotic processes. Here we conducted geochemical, microbiological and genetic analyses of sediments, gases, and pore and surface fluids to characterize fluid processes, community assemblages, functions and activities in a methane-emitting MV of southwestern Taiwan. Multiple lines of evidence suggest that aerobic/anaerobic methane oxidation, sulfate reduction and methanogenesis are active and compartmentalized into discrete, stratified niches, resembling those in marine settings. Surface evaporation and oxidation of sulfide minerals are required to account for the enhanced levels of sulfate that fuels subsurface sulfate reduction and anaerobic methanotrophy. Methane flux generated by in situ methanogenesis appears to alter the isotopic compositions and abundances of thermogenic methane migrating from deep sources, and to exceed the capacity of microbial consumption. This metabolic stratification is sustained by chemical disequilibria induced by the mixing between upward, anoxic, methane-rich fluids and downward, oxic, sulfate-rich fluids.

A shorted square-ring slot antenna with a branched slot is presented for the 1575 MHz and 2.4 GHz dual-band operations. This proposed antenna can be designed by two steps. First, the shorted square-ring slot antenna is designed for circular polarization in the GPS band. Then, a branched slot is added to the original structure to result linear polarization in the 2.4 GHz band. Because the added branched slot almost has no influence in the GPS band's characteristics, the design rule is very simple. The impedance and axial ratio bandwidths for the GPS band is 23.3% and 4.2%, respectively. Besides, the AR and antenna gain is 1.23 dB and 2.3 dBic at the frequency of 1575 MHz. The impedance bandwidth for the 2.4 GHz band is 4.5% and antenna gain at the center frequency of 2.445 GHz is 2.8 dBi. © 2008 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 402–405, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24073

Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.

Shorted square-ring slot antennas with a rectangular slot are presented for the global positioning system (GPS) and third-generation communication (3G) operations.The shorted square-ring slot antenna is used as the basic configuration for circular polarization in the GPS band. Then, an added rectangular slot inside the square-ring slot will radiate linearly polarized wave in the 3G band. Because the added slot has little influence in the GPS band's characteristics, the design rule is very simple. The experimental impedance and axial-ratio bandwidths for the GPS band are 19.8 and 4.5%, respectively. Also, the impedance bandwidth and the antenna gain for the 3G band are 14.9% and 2.5 dBi, respectively. The antenna characteristics such as bandwidths and gain satisfy the dual-band's antenna requirements. Especially, the antenna radiation patterns are very suitable to apply in the GPS and 3G systems. © 2010 Wiley Periodicals, Inc. Microwave Opt Technol Lett 52:855–857, 2010; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.25051

A circularly polarized (CP) patch antenna with gain enhancement is presented. This paper provides a technique to increase the CP gain of an antenna without changing its original configuration. A gain enhancement of 1.7 dBic is achieved by an additional suspended patch. First, we design a CP patch antenna, which works in the band of Wireless Local Area Network (WLAN) with an antenna gain of 10 dBic. Second, adding a suspended patch along the z-axis to the original antenna which the gain enhancement of the modified structure can be improved. The measured and simulated results are equivalent agreement, and they both show that the antenna gain is indeed improved about 1.7 dBic by adding a suspended patch.

As metagenomes are generally composed of sequences from a community of organisms, how to categorize these sequences based on biological features will radically affect the accuracy and sensitivity of the downstream analyses. Thus the sequence binning process is a bottleneck step in the early process of the pipeline of metagenomic characteristics analysis. Several binning approaches have been proposed by using different strategies and features: BLAST using sequence similarity search; k-mer [Sandberg et al., 2001], Self-Organizing Map (SOM) [Abe et al., 2003], and TETRA [Teeling et al., 2004b] using oligonucleotide frequency; and PhyloPythia [McHardy et al., 2007; see also Chapter 40, Vol. I], which is based on Support Vector Machine (SVM), using oligonucleotide frequency and pattern similarity. These methods are either supervised or unsupervised but have their own limitations. Supervised learning methods, such as BLAST, k-mer, SOM, and PhyloPythia, require training datasets, such as completed genomes or labeled long contigs; the unsupervised learning method, TETRA, is intractable for huge datasets because of the required computation on its all-versus-all pairwise comparison matrix. Although these methods have demonstrated their great feasibility on binning task, they were incapable to resolve clusters without identifiable labels. So, we proposed a semisupervised learning method combining a seeding strategy with Growing Self-Organizing Map (GSOM) [Alahakoon et al., 2000], called Seeded GSOM and abbreviated as S-GSOM, for sequence binning. In this study, we have compared S-GSOM with other semisupervised learning methods on the task of sequence clustering. Furthermore, in benchmark datasets, we have shown a higher binning fidelity result with S-GSOM in comparison to other binning methods.

Both bacteria and algal symbionts (genus Symbiodinium), the two major microbial partners in the coral holobiont, respond to fluctuations in the environment, according to current reports; however, little evidence yet indicates that both populations have any direct interaction with each other in seasonal fluctuation. In this study, we present field observations of a compositional change in bacteria and Symbiodinium in the coral Isopora palifera in three separate coral colonies following monthly sampling from February to November in 2008. Using massively parallel pyrosequencing, over 200 000 bacterial V6 sequences were classified to build the bacterial community profile; in addition, the relative composition and quantity of Symbiodinium clades C and D were determined by real-time PCR. The results showed that coral-associated bacterial and Symbiodinium communities were highly dynamic and dissimilar among the tagged coral colonies, suggesting that the effect of host specificity was insignificant. The coral-associated bacterial community was more diverse (Shannon index up to 6.71) than previous estimates in other corals and showed rapid seasonal changes. The population ratios between clade C and D groups of Symbiodinium varied in the tagged coral colonies through the different seasons; clade D dominated in most of the samples. Although significant association between bacteria and symbiont was not detected, this study presents a more detailed picture of changes in these two major microbial associates of the coral at the same time, using the latest molecular approaches.

This paper introduces a set of new algorithms, called the Space-Decomposition Minimization (SDM) algorithms, that decomposes the minimization problem into subproblems. If the decomposed-space subproblems are not coupled to each other, they can be solved independently with any convergent algorithm; otherwise, iterative algorithms presented in this paper can be used. Furthermore, if the design space is further decomposed into one-dimensional decomposed spaces, the solution can be found directly using one-dimensional search methods. A hybrid algorithm that yields the benefits of the SDM algorithm and the conjugate gradient method is also given. An example that demonstrates application of SDM algorithm to the learning of a single-layer perceptron neural network is presented, and five large-scale numerical problems are used to test the SDM algorithms. The results obtained are compared with results from the conjugate gradient method.

Background Prokaryotic microbes, the most abundant organisms in the ocean, are remarkably diverse. Despite numerous studies of marine prokaryotes, the zonation of their communities in pelagic zones has been poorly delineated. By exploiting the persistent stratification of the South China Sea (SCS), we performed a 2-year, large spatial scale (10, 100, 1000, and 3000 m) survey, which included a pilot study in 2006 and comprehensive sampling in 2007, to investigate the biological zonation of bacteria and archaea using 16S rRNA tag and shotgun metagenome sequencing. Results Alphaproteobacteria dominated the bacterial community in the surface SCS, where the abundance of Betaproteobacteria was seemingly associated with climatic activity. Gammaproteobacteria thrived in the deep SCS, where a noticeable amount of Cyanobacteria were also detected. Marine Groups II and III Euryarchaeota were predominant in the archaeal communities in the surface and deep SCS, respectively. Bacterial diversity was higher than archaeal diversity at all sampling depths in the SCS, and peaked at mid-depths, agreeing with the diversity pattern found in global water columns. Metagenomic analysis not only showed differential %GC values and genome sizes between the surface and deep SCS, but also demonstrated depth-dependent metabolic potentials, such as cobalamin biosynthesis at 10 m, osmoregulation at 100 m, signal transduction at 1000 m, and plasmid and phage replication at 3000 m. When compared with other oceans, urease at 10 m and both exonuclease and permease at 3000 m were more abundant in the SCS. Finally, enriched genes associated with nutrient assimilation in the sea surface and transposase in the deep-sea metagenomes exemplified the functional zonation in global oceans. Conclusions Prokaryotic communities in the SCS stratified with depth, with maximal bacterial diversity at mid-depth, in accordance with global water columns. The SCS had functional zonation among depths and endemically enriched metabolic potentials at the study site, in contrast to other oceans. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1434-3) contains supplementary material, which is available to authorized users.