Application of Bioinformatics in Microbial Ecology

The rapid development of high-throughput sequencing technology has greatly promoted the study on microbial diversity. Various bioinformatics softwares were developed and used to analyze the large number of gene information generated from the utilization of this technology. Application of bioinformatics in microbial ecology and the corresponding softwares and databases adopted in α, β-diversity study were summarized in the paper.

Comprehensive comparison of water quality risk and microbial ecology between new and old cast iron pipe distribution systems

The effects of cast iron pipe corrosion onwater quality risk and microbial ecology in drinking water distribution systems(DWDSs)were investigated.It was found that trihalomethane(THMs)concentration and antibiotic resistance genes(ARGs)increased sharply in the old DWDSs.Under the same residual chlorine concentration conditions,the adenosine triphos-phate concentration in the effluent of old DWDSs(Eff-old)was significantly higher than that in the effluent of newDWDSs.Moreover,stronger bioflocculation ability andweaker hy-drophobicity coexisted in the extracellular polymeric substances of Eff-old,meanwhile,iron particles could be well inserted into the structure of the biofilms to enhance the mechanical strength and stability of the biofilms,hence enhancing the formation of THMs.Old DWDSs significantly influenced the microbial community of bulk water and triggered stronger mi-crobial antioxidant systems response,resulting in higher ARGs abundance.Corroded cast iron pipes induced a unique interaction system of biofilms,chlorine,and corrosion prod-ucts.Therefore,as the age of cast iron pipes increases,the fluctuation of water quality and microbial ecology should be paid more attention to maintain the safety of tap water.

Profiling of microbial communities in a bioreactor for treating hydrocarbon-sulfide-containing wastewater

A technology of polymerase chain reaction-denaturing gradient gel electrophoresis(PCR-DGGE)was used to profile the structure and dynamic changes of microbial communities in a bioreactor for treating hydrocarbon-sulfide-containing(HSC)wastewater.The results showed that the heterotrophic genus of Acinetobacter and the autotrophic genera of Thiobacillus and Thiomonas could survive well in all of three operating conditions.Some special genera were also observed with changes of micro-ecoenvironment in the reacto...

The key procedures and advancement in microbial communities analysis of DGGE

Recently, denaturing gradient gel electrophoresis （DGGE） is well established molecular tool in microbial ecology that allows the study of diversity and dynamics of microbial communities. The technique has been gained the preference since reliable facilitative and inexpensive. In order to promote the DGGE further development and make it become a general analysis technique earlier, the key procedures and the advances in microbial communities analysis of DGGE were introduced in this paper.

Biogas by two-stage microbial anaerobic and semi-continuous digestion of Chinese cabbage waste

Anaerobic digestion of Chinese cabbage waste was investigated through a pilot-scale two-stage digester at a mesophilic temperature of 37 ℃. In the acidification digester, the main product was acetic acid, with the maxi- mum concentration of 4289 mg·L^-1 on the fourth day, accounting for 50.32% of total volatile fatty acids. The oxidation reduction potential （ORP） and NH^＋-N level decreased gradually with hydraulic retention time （HRT） of acidification. In the second digestion phase, the maximum methanogenic bacterial concentration reached 9.6 × 10^10ml^-1 at the organic loading rate （OLR） of 3.5-4 kg VS·m^-3, with corresponding HRT of 12-16 days. Accordingly, the optimal biogas production was 0.62 m^3· （kg VS）^-1, with methane content of 65%-68%;. ORP and NH4^＋-N levels in the methanizer remained between -500 and -560 mV and 2000-4500mg· L^-1, respec- tively. Methanococcus and Methanosarcina served as the main methanogens in the anaerobic digester.

Simulating Microbial Functional Diversity Dynamics in Agricultural Soils: An Individual Based Modeling Approach

New agricultural soil model approaches based on the microbiome dynamics must be considered as they can contribute to understand microbiological soil processes directly linked to substrate metabolism and the influence of these processes on plant growth. The present work presents an approach to the modelling of the interactions of the soil microbial functional diversity with the plant in terms of functions associated to specific processes of organic Carbon and Nitrogen metabolism. The substrates transformations arising in the organic matter that enters as a part of an agricultural scheme are the base for define this metabolism. As result, it has been possible to simulate a rhizospheric soil based on the concept of complex system dynamics and Individual Based Modeling known too as Agent-Based Modeling in an agricultural management context. The explicit definition of the microbiome functional diversity and the processing of the structural elements Carbon and Nitrogen, allowed representing the functional dynamics of this complex system composed by microorganisms, Carbon, Nitrogen and the plant. The variables that reflect the biology and the adaptation to the rhizospheric environment characterized the microorganisms and the assemblage community patterns in time. The main simulations output are system glucose and nitrate levels and an approach to plant growth, all resultant from the metabolic process of the considered Carbon and Nitrogen consortia. The results indicate that the microorganism’s diversity assemblages and its functional expression have a fundamental role in terms of plant growth.

Microbial Community and Urban Water Quality

Urbanization of China is substantial and growing, and water resources are crucial for both economic and social sustainable development. Unfortunately, the frequency and intensity of water contamination events are increasing at an unprecedented rate and often accompanied by increased pollutant loading due to human activities such as irreversible industrialization and urbanization. The impacts of human pollution are most evident and of greatest concern at the microbial level. The research of the Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, has been focusing mainly on aquatic microorganisms in the urban environment, from drinking water and landscape water to waste water. Its projects fall into three categories: biomonitoring and bioassessment, microbial ecology and diversity, ecotoxicology and environmental microbiology. Its scientif ic topics include the aquatic ecological safety and microbial food web.

Ecological effects of the microbial weathering of silicate minerals

1 Introduction Global climate change is one of the greatest challenges facing humankind in the 21st century.Studying,and utilising,the carbon sink caused by the weathering of silicate minerals has been a key research focus for

Linking bacterial and archaeal community dynamics to related hydrological,geochemical and environmental characteristics between surface water and groundwater in a karstic estuary

Subterranean estuaries(STEs)are characterized by the mixing of terrestrial fresh groundwater and seawater in coastal aquifers.Although microorganisms are important components of coastal groundwater ecosystems and play critical roles in biogeochemical transformations in STEs,limited information is available about how their community dynamics interact with hydrological,geochemical and environmental characteristics in STEs.Here,we studied bacterial and archaeal diversities and distributions with 16S rRNA-based Illumina MiSeq sequencing technology between surface water and groundwater in a karstic STE.Principal-coordinate analysis found that the bacterial and archaeal communities in the areas where algal blooms occurred were significantly separated from those in other stations without algal bloom occurrence.Canonical correspondence analysis showed that nutrients and salinity can explain the patterns of bacterial and archaeal community dynamics.The results suggest that hydrological,geochemical and environmental characteristics between surface water and groundwater likely control the bacterial and archaeal diversities and distributions in STEs.Furthermore,we found that some key species can utilize terrestrial pollutants such as nitrate and ammonia in STEs,indicating that these species(e.g.,Nitrosopumilus maritimus,Limnohabitans parvus and Simplicispira limi)may be excellent candidates for in situ degradation/remediation of coastal groundwater contaminations concerned with the nitrate and ammonia.Overall,this study reveals the coupling relationship between the microbial communities and hydrochemical environments in STEs,and provides a perspective of in situ degradation/remediation for coastal groundwater quality management.

Spatial-temporal dynamics of bacterioplankton communities in the breeding area of large yellow croaker Larimichthys crocea in Sansha Bay,China

As an important spawning ground for large yellow croaker Larimichthys crocea,Sansha Bay,South China Sea has been a research hotspot.However,studies on the influence of the bacterioplankton community and assessments of its seasonal succession of bacterioplankton in different sea areas in Sansha Bay are still limited.To address the issue,we use 16S rRNA gene amplicon sequencing and functional prediction to investigate the spatial-temporal dynamics of the bacterioplankton community in three distinct areas,i.e.,Breeding Area(BA),Yantian Harbor(YH),and Bay Margin(BM)of Sansha Bay.Results show that the structure of the bacterioplankton community in Sansha Bay had a significant seasonal succession.Moreover,the representative zero-radius Operation Taxon Units in different seasons were significantly different among the three selected sea areas.Specifically,during the breeding season,bacterioplankton communities in BA were characterized by compound-degrading bacteria,such as Rhodococcus and Owenweeksia,while in YH and BM,animal parasites or symbionts such as Vibrio and Arcobacter were dominant.Furthermore,the redundancy analysis and Spearman correlation analysis further explained that water temperature,dissolved oxygen,and ammonia nitrogen were the main environmental factors responsible for the difference.In addition,the bioindicator functions screened by Functional Annotation of Prokaryotic Taxa and random forest machine learning mainly relied on compound degradation,nitrite oxidation,and photoheterotrophy.The compound-degradationcorresponded bacterioplankton genera such as Rhodococcus had relatively higher abundance in BM,while Nitrospina corresponding to nitrite oxidation tended to be abundant in YH and BA.Based on the spatial and temporal variation in the composition and function of bacterioplankton,our findings provide a basis for understanding the theory of bacterioplankton community structure in the inner-bay habitat of the large yellow croaker in Sansha Bay.

Different no-till grain production systems with Urochloa spp.affect soil microbial community structure,biomass and activity in a tropical Ultisol

Integrated grain cropping systems promote soil health(SH)and sustainability.Microbial biomass and activity(MBA)and community structure(MCS)are key to SH.Integration of maize with Urochloa pastures strongly impacts MBA and MCS.MBA is more sensitive than MCS to shifts in grain cropping systems.Systems under continuous Urochloa increased microbial activity and AMF abundance.Tropical soils are prone to degradation.Adoption of conservation agricultural practices is essential to improve soil health,which is influenced by soil microbes.In this study we analyzed shifts in microbial biomass and activity(MBA)and microbial community structure(MCS)based on fatty acid methyl esthers(FAMEs)between five no-till agricultural practices:maize monoculture(MM);maize annualy intercropped with Urochloa decumbens(M/Ud);M/Ud with soybean rotation every other year(M/Ud-S);M/Ud keeping the pasture for the next two years(M/Ud-Ud-Ud);and maize intercropped with U.ruziziensis keeping the pasture for the next two years(M/Ur-Ur-Ur).Results indicated that MBA was affected by the inclusion of Urochloa intercropping and by rotation with soybean.Systems under a longer residence time with Urochloa in the field had higherβ-glucosidase activity and soil basal respiration,indicating a greater microbial activity.MCS was less affected than MBA by the investigated cropping systems.MCS changed only in the continuous pasture systems,which were enriched in arbuscular mycorrhyzal fungi(AMF).Additionally,the continuous pasture systems had lower microbial stress ratios than the other agricultural practices.In sum,our study showed that utilization of Urochloa spp.under longer periods in no-till agricultural practices contributes to increase microbial activity,AMF abundance and decrease microbial stress ratio.These changes are primarily beneficial for soil health.

Research on Mechanism and Application of DUAN-NAI-AN on Controlling Weaned Piglet Diarrhea

[ Objective] The study aimed to explore the function mechanism of microbial ecological agent DUAN-NAI-AN on controlling weaned piglet diarrhea. E Method] DUAN-NAI-AN was given to the weaned piglets by oral administration and its effects on diarrhea rate, growth performance, in- testinal microflora, pH values of different parts of the intestine and intestinal mucosal morphology were observed. [ Result] DUAN-NAI-AN could im- prove the growth performance of weaned piglets by increasing the growth rate and phase weight gain, showing as higher livability, average daily gain and daily feed intake as well as lower diarrhea rate with 19.24% decline by contrast to the control. In addition, DUAN-NAI-AN could keep the intestinal mucosal mechanical barrier and normal digestive function by strengthening intestinal resistance and thus enhance the intestinal mucosal im- mune level. It could also decrease the proportion of potential pathogens and their toxicity effects inside the intestine to help the piglets transfer to and then maintain the dynamic balance of intestinal microflora in a very short period, and it also showed a trend of decreasing the pH value of piglet in- testinal contents. [ Conclusion] DUAN-NAI-AN is an effective microbial ecological agent for the control of weaned piglet diarrhea.

A Technological Overview of Biogas Production from Biowaste

The current irrational use of fossil fuels and the impact of greenhouse gases on the environment are driving research into renewable energy production from organic resources and waste. The global energy demand is high, and most of this energy is produced from fossil resources. Recent studies report that anaerobic di- gestion （AD） is an efficient alternative technology that combines biofuel production with sustainable waste management, and various technological trends exist in the biogas industry that enhance the production and quality of biogas. Further investments in AD are expected to meet with increasing success due to the low cost of available feedstocks and the wide range of uses for biogas （i.e., for heating, electricity, and fuel）. Bio- gas production is growing in the European energy market and offers an economical alternative for bioenergy production. The objective of this work is to provide an overview of biogas production from lignocellulosic waste, thus providing information toward crucial issues in the biogas economy.

Progress toward understanding the contribution of alkali generation in dental biofilms to inhibition of dental caries

Alkali production by oral bacteria is believed to have a major impact on oral microbial ecology and to be inibitory to the initiation and progression of dental caries. A substantial body of evidence is beginning to accumulate that indicates the modulation of the alkalinogenic potential of dental biofilms may be a promising strategy for caries control. This brief review highlights recent progress toward understanding molecular genetic and physiologic aspects of important alkali-generating pathways in oral bacteria, and the role of alkali production in the ecology of dental biofilms in health and disease.

Temporal dynamics of phytoplankton communities in a semi-enclosed mariculture pond and their responses to environmental factors

Variations in physical-chemical factors, species composition, abundance and biomass of nano-and micro-phytoplankton assemblages, as well as their responses to environmental factors, were investigated over a complete cycle (6 months) in a semi-enclosed shrimp-farming pond near Qingdao, northern China. The aim was to establish the temporal patterns of phytoplankton communities and to evaluate protists as suitable bioindicators to water quality in mariculture systems. A total of 34 taxa with nine dominant species were identified, belonging to six taxonomic groups (dinoflagellates, diatoms, cryptophyceans, chlorophyceans, euglenophyceans and chrysophyceans). A single peak of protist abundance occurred in October, mainly due to chlorophyceans, diatoms and chrysophyceans. Two biomass peaks in July and October were primarily due to dinoflagellates and diatoms. Temporal patterns of the phytoplankton communities significantly correlated with the changes in nutrients, temperature and pH, especially phosphate, either alone or in combination with NO3-N and NH3-N. Species diversity, evenness and richness indices were clearly correlated with water temperature and/or salinity, whereas the biomass/abundance ratio showed a significant correlation with NO3-N. The results suggest that phytoplankton are potentially useful bioindicators to water quality in semi-enclosed mariculture systems.

Molecular diversity and biogeography of benthic microeukaryotes in temperate seagrass(Zostera japonica)systems of northern China

The productivity and health of seagrass depend on the combined inputs of nutrients from the water and sediments in which they grow and the microbiota with which they live intimately.However,little is known about the composition and diversity pattern of single-celled benthic eukaryotes in seagrass meadows.Here,we investigated how the structure and diversity of the benthic microeukaryotic community vary with respect to season,location,and seagrass colonization,by applying 18S rRNA gene amplicon sequencing for 96 surface sediment samples that were collected from three different seagrass habitats through four seasons.We found that benthic microeukaryotic communities associated with seagrass Zostera japonica exhibited remarkable spatial and seasonal variations,as well as differences between vegetated and unvegetated sediments.Diatoms and dinoflagellates predominated in the benthic microeukaryotic communities,but they were inversely correlated and displaced each other as the dominant microbial group in different seasons or habitats.Mucoromycota was more prevalent in vegetated sediments,whereas Lobulomycetales and Chytridiales had higher proportions in unvegetated sites.Total organic carbon and total organic nitrogen were the most important environmental factors in driving the microeukaryotic assemblages and diversity.Our study expands the available knowledge on the biogeographic distribution patterns and niche preferences for benthic microeukaryotes in seagrass systems.

Planktonic protist communities in semi-enclosed mariculture waters: temporal dynamics of functional groups and their responses to environmental conditions

The functional groups of planktonic protist communities and their responses to the changes of environmental conditions were investigated in a semi-enclosed shrimp-farming pond in Qingdao,Shandong Province,China,during a six-month study period （a complete shrimp-culture cycle） from May to October 2002.The results reveal that： （1） the protist communities represented five trophic and functional groups of the species identified,about 60% were photoautotrophs,20% algivores,12% bacterivores,5% raptors and about 3% non-selectives;（2） the photoautotrophs,algivores and bacterivores were the primary contributors to the changes in the protist communities in short temporal scales,the succession of dominance typically being bacterivores→photoautotrophs→algivores,with the raptors dominating the protist communities in a single sample （early June）;（3） the photoautotrophs and non-selectives were the primary contributors to the peak of protist abundance in early October whereas the photoautotrophs,bacterivores,raptors and non-selectives mainly gave rise to two bimodal peaks of biomass in July and October respectively;（4） five functional groups of protist communities represented significant correlations with water nutrients （i.e.,NH 3-N,NO 3-N,and PO 4 ）,either alone or in combination with temperature,of which algivores and raptors were strongly correlated with phosphate and the concentration of Chl a,while bacterivores were strongly related to nitrogen and the concentration of bacteria.These findings confirm that planktonic protists are potentially useful bioindicators of water quality in the semi-enclosed mariculture system.

Temporal species distributions of planktonic protist communities in semi-enclosed mariculture waters and responses to environmental stress

In order to evaluate the relationships between temporal species succession of planktonic protists and physical-chemical parameters in semi-enclosed mariculture waters, species distributions in response to environmental stress were investigated in a shrimp-farming pond near Qingdao, China during a complete shrimp-culture cycle （May to October 2002）. A clear temporal succession in species distribution was found over the complete farming cycle. For example, before the introduction of the shrimp larvae there was low-variability of species distribution in the protist communities whereas during the stages immediately after, there was higher variability in species composition. Multiple linear/logistic regression analyses demonstrate that 12 protist taxa （e.g., Gyrodinium spirale, Teleaulax acuta, Prorocentrum spp. and Mesodinium pupula） were related to the nutrients, in particular ammonia and phosphates, alone or in combination with water temperature. These results suggest that temporal variations in species distribution of planktonic protist communities might be used in assessing water quality of semi-enclosed mariculture waters.

Analysis of Microbial Molecular Ecology Techniques in Constructed Rapid Infiltration System

The microbial molecular ecology techniques, which were developed on the basis of molecular, were applied in studying the bacteria in Constructed Rapid Infiltration （CRI） system. These techniques are very efficient in better describing the bacterial diversity, microbial community distribution, and relations between microbial group structure and nitrogen contamination through the analysis of microbial nucleic acid sequence fragment in CRI. The results further revealed the removal mechanism of contamination, which is essential for the improvement of wastewater treatment in CRI.