Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments

In Vitro Screening of Molecular Diversity Among Sorghums (Sorghum bicolor (L.) Landraces in Marathwada Region by Molecular Markers

Allelic variation is a valuable tool for displaying high levels of polymorphism within species and is closely correlated with crop productivity. In Marathawada, there is a significant amount of phenotypic heterogeneity among sorghum landraces. However, molecular variability needs to be reevaluated in order to identify any potential barriers that can interfere with current improvement initiatives. In the current work, we used 5 SSR markers to categorize 20 genotypes of elite (Sorghum bicolor L. Moench) accession from the Marathwada region, including one standard cultivar from various agro-economic zones. According to the results of this study, 14 alleles were found among the 20 genotypes, with a PIC value that ranged from 0.37 to 0.70 and a mean of 0.44 per locus. Each locus had anything from 1 (gpsb089) and 5 (mSbCIR223), with an average of 2.80 alleles per locus. A neighbor-joining tree was constructed and showed clustering of genotypes into two groups; this indicates that there is considerable diversity in genotypes compared with advanced cultivar for desired genotype (IS1042) by using SSR markers. Results show that most diverse cultivars were IS-4564, IS18357, and IS-18381, and significant variation was also reported in IS4566 and IS18379.

Spatio-temporal connectivity of a toxic cyanobacterial community and its associated microbiome along a freshwater-marine continuum

Due to climate changes and eutrophication, blooms of predominantly toxic freshwater cyanobacteria are intensifying and are likely to colonize estuaries, thus impacting benthic organisms and shellfish farming representing a major ecological, health and economic risk. In the natural environment, Microcystis form large mucilaginous colonies that influence the development of both cyanobacterial and embedded bacterial communities. However, little is known about the fate of natural colonies of Microcystis by salinity increase. In this study, we monitored the fate of a Microcystis dominated bloom and its microbiome along a French freshwater-marine gradient at different phases of a bloom. We demonstrated changes in the cyanobacterial genotypic composition, in the production of specific metabolites (toxins and compatible solutes) and in the heterotrophic bacteria structure in response to the salinity increase. In particular M. aeruginosa and M. wesenbergii survived salinities up to 20. Based on microcystin gene abundance, the cyanobacteria became more toxic during their estuarine transfer but with no selection of specific microcystin variants. An increase in compatible solutes occurred along the continuum with extensive trehalose and betaine accumulations. Salinity structured most the heterotrophic bacteria community, with an increased in the richness and diversity along the continuum. A core microbiome in the mucilage-associated attached fraction was highly abundant suggesting a strong interaction between Microcystis and its microbiome and a likely protecting role of the mucilage against an osmotic shock. These results underline the need to better determine the interactions between the Microcystis colonies and their microbiome as a likely key to their widespread success and adaptation to various environmental conditions.

In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay

Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.

On-farm soil resistome is modified after treating dairy calves with the antibiotic florfenicol

We determined the immediate impact of exposure to antibiotic-treated animals on housing soil microbiome and resistome. Fecal (n = 36) and soil (n = 108) samples from dairy calves (n = 6) treated with and without florfenicol over 30 days were collected. There were temporary changes in the gut microbiome of antibiotic-treated calves as measured by Shannon diversity (16S rRNA gene sequencing; P = 0.03), but not in the housing soil microbiome (P > 0.05). Droplet-digital PCR demonstrated that floR gene increased by 1-log in soil exposed to treated animals (P < 0.001), but it remained relatively stable in the control soil whereby calves were not treated with antibiotic. Resistome in exposed soil was largely modified (P = 0.004) with the overall prevalence of antimicrobial resistance genes (ARGs) significantly elevated (3.8-fold increase by day 10; P = 0.01). In addition to florfenicol, enriched ARGs collectively conferring resistance to tetracyclines, aminoglycosides, sulfonamides, elfamycins, macrolides-lincosamides-streptrogramin A/B, and beta-lactams. Quantitative PCR validated that ARGs including str and tetG in soil exposed to florfenicol-treated calves had gradually increased fold-change difference relative to the control soil over time. Moreover, a greater diversity of transferrable ARGs was observed in exposed soil and these were associated with a greater diversity of bacterial species. Evaluation of on-farm effects to soil in situ after exposure to antibiotic-treated animals can help design effective managements to mitigate antibiotic resistance in food-animal production.

Microcosm study of atrazine bioremediation by indigenous microorganisms and cytotoxicity of biodegraded metabolites

Intensive use of atrazine in agriculture to increase crop productivity has resulted in pollution and consequently deteriorated the environment. Three isolated bacteria, Rhodococcus sp. BCH2 (RB), Bacillus sp. PDK1 (BP1) and Bacillus sp. PDK2 (BP2) possessing capability to degrade atrazine were used in different combinations (RB + BP1, RB + BP2, BP1 + BP2, RB + BP1 + BP2) to prepare a highly effective bacterial consortium which can significantly reduce the toxicity of atrazine. Cytotoxicity tests evaluated by MTT assay on HepG2 indicated significant decrease in the toxicity of atrazine by the consortium RB + BP1 + BP2 due to its effective degradation and formation of simpler and less/nontoxic metabolites compared to other combinations of consortia. A microcosm study was conducted to check the survivability of this consortium (RB + BP1 + BP2) in the presence of atrazine and indigenous soil microflora for four weeks. LC-Q-TOF/MS analysis revealed that RB + BP1 + BP2 could degrade atrazine to various simple metabolites in the microcosm. The cluster analysis of the DGGE patterns of the microcosm of control-soil, soil exposed to atrazine and soil augmented with consortium in the presence of atrazine (1000 mg kg^-1) revealed a shift in microbial community of soil. The microbial dynamics studies suggested that the augmented bacteria were well-thrived with natural microflora during four weeks of exposure to atrazine.

Application of Denaturing Gradient Gel Electrophoresis to the Analysis of Bacterial Communities Associated With Asymptomatic and Symptomatic Pericoronitis

PURPOSE

Denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial communities associated with asymptomatic and symptomatic pericoronitis. The aim of the study was to compare the fingerprinting patterns of these 2 clinical conditions.

MATERIALS AND METHODS

The microbiota of mandibular third molar pockets associated with asymptomatic or symptomatic pericoronitis cases were collected and profiled by the polymerase chain reaction DGGE method. Banding patterns were compared by cluster analysis techniques.

RESULTS

Thirteen symptomatic pericoronitis and 7 asymptomatic pericoronitis samples were collected. Comparative analysis of the 2 clinical conditions showed bands that were common to the symptomatic and asymptomatic cases, but most DGGE bands appeared to be unique to the clinical condition. No single band occurred in all profiles. The mean number of bands detected in the 16S rDNA community profiles was 23.8 ± 4.2 (range, 19 to 34) for samples from symptomatic cases and 24.1 ± 2.4 (range, 21 to 29) for those from asymptomatic cases. Cluster analysis and multidimensional scaling analysis of the DGGE banding pattern showed a distinction in the similarity of banding patterns according to the presence or absence of symptoms.

CONCLUSIONS

These results suggest that the diversity of pericoronal pocket microbiota in asymptomatic pericoronitis cases differs markedly from that of symptomatic cases.

Structure and temporal dynamics of the bacterial communities associated to microhabitats of the coral Oculina patagonica

Corals are known to contain a diverse microbiota that plays a paramount role in the physiology and health of holobiont. However, few studies have addressed the variability of bacterial communities within the coral host. In this study, bacterial community composition from the mucus, tissue and skeleton of the scleractinian coral Oculina patagonica were investigated seasonally at two locations in the Western Mediterranean Sea, to further understand how environmental conditions and the coral microbiome structure are related. We used denaturing gradient gel electrophoresis in combination with next-generation sequencing and electron microscopy to characterize the bacterial community. The bacterial communities were significantly different among coral compartments, and coral tissue displayed the greatest changes related to environmental conditions and coral health status. Species belonging to the Rhodobacteraceae and Vibrionaceae families form part of O. patagonica tissues core microbiome and may play significant roles in the nitrogen cycle. Furthermore, sequences related to the coral pathogens, Vibrio mediterranei and Vibrio coralliilyticus, were detected not only in bleached corals but also in healthy ones, even during cold months. This fact opens a new view onto unveiling the role of pathogens in the development of coral diseases in the future.

Development of cecal-predominant microbiota in broilers during a complete rearing using denaturing gradient gel electrophoresis

Understanding of the intestinal microbiota is crucial to enhance intestinal health and performance parameters in animals. A more exhaustive research of the intestinal microbiota of broilers could be of interest to implement appropriate intervention measures. The aim of the present study was to investigate the development of the predominant cecal microbiota in broilers that were fed a Lactobacillus salivarius DSPV 001P strain during a complete rearing using denaturing gradient gel electrophoresis (DGGE). Bacterial DNA from cecal samples of 24 broilers at different ages were amplified by PCR and analysed by DGGE. A total of 35 DGGE products were excised and sequenced. Distinctive differences in bacterial communities were observed in the caecum as broilers age. At early stages, identified bacteria within the caecum of broilers were predominantly Clostridium-related species. Also, some sequences had the closest match to the genus Escherichia/Shigella. Furthermore, the caecum was a reservoir rich in uncultured bacteria. The major difference observed in our study was an increase of potentially beneficial Lactobacillus at Day 45. These results may be attributed to modulation of the microbiota by the probiotic supplementation. The obtained data could be relevant for future studies related to the influence of the microbiota resulting from probiotic supplementation on the performance and the immunological parameters of broilers.

Abundance of Common Aerobic Anoxygenic Phototrophic Bacteria in a Coastal Aquaculture Area

Aerobic anoxygenic phototrophic bacteria (AAnPB) rely on not only heterotrophic but also phototrophic energy gain. AAnPB are known to have high abundance in oligotrophic waters and are the major portion of the bacterial carbon stock in the environment. In a yearlong study in an aquaculture area in the Uwa Sea, Japan, AAnPB, accounted for 4.7 to 24% of the total bacteria by count. Since the cell volume of AAnPB is 2.23 ± 0.674 times larger than the mean for total bacteria, AAnPB biomass is estimated to account for 10–53% of the total bacterial assemblage. By examining pufM gene sequence, a common phylogenetic AAnPB species was found in all sampling sites through the year. The common species and other season-specific species were phylogenetically close to unculturable clones recorded in the Sargasso Sea and Pacific Ocean. The present study suggests that the common species may be a cosmopolitan species with worldwide distribution that is abundant not only in the oligotrophic open ocean but also in eutrophic aquaculture areas.

Novel Bacterial Phylotypes in Endodontic Infections

Although molecular studies have revealed potential oral pathogens among the phyla Spirochaetes and Deferribacteres, their occurrence in endodontic infections has not been consistently investigated. In this study, we devised a nested PCR-DGGE approach to survey samples from infected root canals for the presence of members of these two phyla, and to examine their diversity. The primers used also amplified DNA from Atopobium species. Eight of 10 cases showed bands representative of the target bacterial groups. DGGE profiles revealed a mean number of 6.5 intense and faint bands. No single band occurred in all profiles. Sequences from intense bands excised from the gel showed similarities to species/phylotypes of all target groups— Flexistipes species ( Deferribacteres phylum), uncharacterized spirochetes, and Atopobium species. Analysis of these data indicates that uncultivated Spirochaetes and Deferribacteres phylotypes are frequent members of the endodontic microbiota and may be potential pathogens involved with the etiology of periradicular diseases.

Microbial diversity in an anaerobic digester with biogeographical proximity to geothermally active region

Anaerobic digestion of agricultural biomass or wastes can offer renewable energy, to help meet the rise in energy demands. The performance of an anaerobic digester considerably depends upon the complex interactions between bacterial and archaeal microbiome, which is greatly influenced by environmental factors. In the present study, we evaluate a microbial community of digester located at two different geographical locations, to understand whether the biogeographical proximity of a digester to a geothermally active region has any influence on microbial composition. The comparative microbial community profiling, highlights coexistence of specific bacterial and archaeal representatives (especially, Prosthecochloris sp., Conexibacter sp., Crenarchaeota isolate (Caldivirga sp.), Metallosphaera sp., Pyrobaculum sp. and Acidianus sp.) in a digester with close proximity to geothermally active region (Site I) and their absence in a digester located far-off from geothermally active region (Site II). A Sörensen's index of similarity of 83.33% and 66.66% for bacterial and archaeal community was observed in both the reactors, respectively.

RT-PCR-DGGE Analysis to Elucidate the Dominant Bacterial Species of Industrial Spanish-Style Green Table Olive Fermentations

This paper describes the dominant bacterial species metabolically active through the industrial production of Spanish-style Manzanilla and Gordal olives. For this purpose, samples (brines and fruits) obtained at 0, 15, and 90 fermentation days were analyzed by a culture-independent approach to determine viable cells by reverse transcription of RNA and further PCR-DGGE analysis, detecting at least 7 different species. Vibrio vulnificus, Lactobacillus plantarum group, and Lactobacillus parafarraginis were present in samples from both cultivars; Lactobacillus sanfranciscensis and Halolactobacillus halophilus were detected only in Gordal samples, while Staphylococcus sp. was exclusively found at the onset of Manzanilla fermentations. Physicochemical data showed a typical fermentation profile while scanning electron microscopy confirmed the in situ biofilm formation on the olive epidermis. Different Bacillus, Staphylococcus, and Enterococcus species, not detected during the fermentation process, were also found in the solid marine salt used by the industry for preparation of brines. Elucidation of these non-lactic acid bacteria species role during fermentation is then an appealingly challenge, particularly regarding safety issues.

Decreased microbial diversity and Lactobacillus group in the intestine of geriatric giant pandas (Ailuropoda melanoleuca)

It has been established beyond doubt that giant panda genome lacks lignin-degrading related enzyme, gastrointestinal microbes may play a vital role in digestion of highly fibrous bamboo diet. However, there is not much information available about the intestinal bacteria composition in captive giant pandas with different ages. In this study, we compared the intestinal bacterial community of 12 captive giant pandas from three different age groups (subadults, adults, and geriatrics) through PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbial diversity in the intestine of adults was significantly higher than that of the geriatrics (p < 0.05), but not significant compared to the subadults (p > 0.05). The predominant bands in DGGE patterns shared by the twelve pandas were related to Firmicutes and Proteobacteria. Additionally, in comparison to healthy individuals, antibiotic-treated animals showed partial microbial dysbiosis. Real-time PCR analyses confirmed a significantly higher abundance of the Lactobacillus in the fecal microbiota of adults (p < 0.05), while other bacterial groups and species detected did not significantly differ among the three age groups (p > 0.05). This study revealed that captive giant pandas with different ages showed different intestinal bacteria composition.

Bacterial community structures of deep-sea water investigated by molecular biological techniques

The aim of the present study was to investigate the bacterial community structures of deep-sea water (DSW) and surface seawater (SSW) samples in Japan by molecular biological techniques. DGGE analyses and pyrosequencing analysis revealed that bacterial community structures of DSW were diverse and differed from those of SSW. This is the first report on the horizontal variation of bacterial community structures of DSW throughout Japan. In addition, pyrosequencing analysis revealed that the number of phyla in DSW was larger than that in SSW, and specific phyla, such as Firmicutes and Planctomycetes, were characterized by a higher proportion of the bacterial community structure in DSW than in SSW. Taken together, these results indicate that a variety of bacteria that are specifically adapted to the DSW environments can be expected to be found in DSW, and DSW would thus be a potential resource for novel or unique microorganisms and compounds.

Changes in Fecal and Colonic Mucosal Microbiota of Patients with Refractory Constipation after a Subtotal Colectomy

The purpose of this study was to investigate the changes in gut microbiota of patients with refractory constipation 6 months after a subtotal colectomy. Feces and mucosal samples of five healthy volunteers and 17 patients with refractory constipation before and six months after subtotal colectomy were collected. Denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction techniques were used for quantitative analysis of main bacterial groups and archeal methanogens. No significant differences were found in the DGGE profiles among the three groups. After subtotal colectomy, a significantly decreased similarity coefficient was observed in the fecal. The Shannon diversity indices had no significant differences among the three groups. The numbers of predominant bacteria (Bacteriodetes, Clostridium coccoides group, and Clostridium leptum group) did not significantly change in patients before and after surgery compared with healthy control subjects, and the number of total bacteria, Firmicutes, Bacteriodetes, and Clostridium leptum group bacteria in the feces decreased after surgery. However, the numbers of these bacteria remained the same in mucosa from postoperative patients. The numbers of Bifidobacteria and Lactobacilli in feces and the number of Bifidobacteria in mucosa were significantly lower in preoperative compared with healthy control subjects and increased after the surgery. The number of methanogens in the mucosa was decreased in preoperative patients but returned to normal levels postoperatively. In conclusion, although there was no difference in the structure of the predominant bacteria between refractory constipated patients and healthy control subjects, the number of probiotics ( Bifidobacteria and Lactobacilli) was significantly lower in refractory constipated patients. However, subtotal colectomy can significantly normalize the number of intestinal flora.

Brine assemblages of ultrasmall microbial cells within the ice cover of Lake Vida, Antarctica

The anoxic and freezing brine that permeates Lake Vida's perennial ice below 16 m contains an abundance of very small (≤0.2-μm) particles mixed with a less abundant population of microbial cells ranging from >0.2 to 1.5 μm in length. Fluorescent DNA staining, electron microscopy (EM) observations, elemental analysis, and extraction of high-molecular-weight genomic DNA indicated that a significant portion of these ultrasmall particles are cells. A continuous electron-dense layer surrounding a less electron-dense region was observed by EM, indicating the presence of a biological membrane surrounding a cytoplasm. The ultrasmall cells are 0.192 ± 0.065 μm, with morphology characteristic of coccoid and diplococcic bacterial cells, often surrounded by iron-rich capsular structures. EM observations also detected the presence of smaller unidentified nanoparticles of 0.020 to 0.140 μm among the brine cells. A 16S rRNA gene clone library from the brine 0.1- to 0.2-μm-size fraction revealed a relatively low-diversity assemblage of Bacteria sequences distinct from the previously reported >0.2-μm-cell-size Lake Vida brine assemblage. The brine 0.1- to 0.2-μm-size fraction was dominated by the Proteobacteria-affiliated genera Herbaspirillum, Pseudoalteromonas, and Marinobacter. Cultivation efforts of the 0.1- to 0.2-μm-size fraction led to the isolation of Actinobacteria-affiliated genera Microbacterium and Kocuria. Based on phylogenetic relatedness and microscopic observations, we hypothesize that the ultrasmall cells in Lake Vida brine are ultramicrocells that are likely in a reduced size state as a result of environmental stress or life cycle-related conditions.

Effects of a nutrient additive on the density of functional bacteria and the microbial community structure of bioorganic fertilizer

In this study, a secondary composting experiment was conducted to investigate the effects of concentrated monosodium glutamate wastewater (CMGW) as a nutrient additive on enhancing the density of functional bacteria in bioorganic fertilizer (BOF). The results showed that, as the CMGW was added, the composting mixture temperature rose more quickly and strongly, and the functional bacteria Bacillus subtilis F2 percentage in spores increased significantly. Furthermore, both the highest species richness value (Rs) of a given sample and similarity coefficient value (Cs) between a sample and strain F2 based on DGGE analysis were also observed in the treatment with CMGW. A similar effect of CMGW on the microbial community structure was verified by means of illumine-MiSeq sequencing. It may thus be concluded that CMGW is a recommendable nutrient additive for F2 predominating in the secondary composting process.

Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing

The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. A total of 188,623 optimized reads and 15,527 operational taxonomic units (OTUs) were obtained from the ten gut contents samples and four surface sediment samples. The sequences in the sediments, foregut contents, and hindgut contents were assigned to 38.0±4.7, 31.2±6.2 and 27.8±6.5 phyla, respectively. The bacterial richness and Shannon diversity index were both higher in the ambient sediments than in the gut contents. Proteobacteria was the predominant phylum in both the gut contents and sediment samples. The predominant classes in the foregut, hindgut, and ambient sediment were Holophagae and Gammaproteobacteria, Deltaproteobacteria and Gammaproteobacteria, and Gammaproteobacteria and Deltaproteobacteria, respectively. The potential probiotics, including sequences related to Bacillus, lactic acid bacteria (Lactobacillus, Lactococcus, and Streptococcus) and Pseudomonas were detected in the gut of A. japonicus. Principle component analysis and heatmap figure showed that the foregut, hindgut, and ambient sediment respectively harbored different characteristic bacterial communities. Selective feeding of A. japonicus may be the primary source of the different bacterial communities between the foregut contents and ambient sediments.

Community composition of the Planctomycetes associated with different macroalgae

Insights into the diversity of marine natural microbial biofilms, as for example those developing at the surface of marine macroalgae, can be obtained by using molecular techniques based on 16S rRNA genes. We applied denaturing gradient gel electrophoresis (DGGE) with 16S rRNA genes-specific primers for Planctomycetes to compare the communities of these organisms developing on six different macroalgae (Chondrus crispus, Fucus spiralis, Mastocarpus stellatus, Porphyra dioica, Sargassum muticum, and Ulva sp.) sampled in spring 2012 in two rocky beaches in the north of Portugal. Planctomycetes can be one of the dominant organisms found in the epibacterial community of macroalgae, and we wanted to determine the degree of specificity and the spatial variation of these group. Shannon diversity indexes obtained from the comparison of DGGE profiles were similar in all the macroalgae, and in both sites, F. spiralis was the algae presenting lower Planctomycetes diversity, while M. stellatus and P. dioica from Porto showed the highest diversity. The analysis of DGGE profiles, including anosim statistics, indicate the existence of a specific Planctomycetes community associated with the algal host, likely independent of geographical variation. Sequencing of DGGE bands indicated that Planctomycetes communities were highly diverse, and some Operational Taxonomic Units seemed to be specifically associated with each macroalgae.

Effect of high loading on substrate utilization kinetics and microbial community structure in super fast submerged membrane bioreactor

The study investigated the effect of high substrate loading on substrate utilization kinetics, and changes inflicted on the composition of the microbial community in a superfast submerged membrane bioreactor. Submerged MBR was sequentially fed with a substrate mixture and acetate; its performance was monitored at steady-state, at extremely low sludge age values of 2.0, 1.0 and 0.5d, all adjusted to a single hydraulic retention time of 8.0 h. Each MBR run was repeated when substrate feeding was increased from 200 mg COD/L to 1000 mg COD/L. Substrate utilization kinetics was altered to significantly lower levels when the MBR was adjusted to higher substrate loadings. Molecular analysis of the biomass revealed that variable process kinetics could be correlated with parallel changes in the composition of the microbial community, mainly by a replacement mechanism, where newer species, better adapted to the new growth conditions, substituted others that are washed out from the system.

Effects of alfalfa meal on the intestinal microbial diversity and immunity of growing ducks

This study was conducted to investigate the effects of alfalfa meal diets on the intestinal microbial diversity and immunity of growing egg-type ducks. A total of 128 healthy 7-week-old female egg-type Shaoxing ducks were selected and randomly assigned into four dietary treatments: 0%, 3%, 6% and 9% alfalfa meal for 8 weeks. Each treatment consisted of four replicates of eight ducks each. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to characterize the microbiota. The results showed that the DGGE fingerprints of the V6-V8 fragments of the 16S rRNA from the caeca and faeces of ducks fed 3%, 6% and 9% alfalfa meal had significantly higher microbiota species richness than those fed 0% alfalfa meal (p < 0.05). The Shannon-Weiner index of the microbiota from the caeca and faeces of ducks fed 3%, 6% and 9% alfalfa meal was significantly higher than those fed 0% alfalfa meal (p < 0.05). Molecular analysis of the caecal and faecal DNA extracts showed that the alfalfa meal diet promotes the intestinal microbial diversity, as indicated by their higher species richness and Shannon-Weiner index. However, the groups did not significantly differ in terms of average daily gain, feed intake and gain-to-feed ratio (p > 0.05), and the 3-9% alfalfa meal did not affect the growth performance of the growing egg-type ducks. The proliferation of T and B lymphocytes was significantly greater (p < 0.05) in the groups supplemented with 3%, 6% and 9% of alfalfa meal than the unsupplemented control group, and alfalfa meal promoted the lymphocytes proliferation of the growing egg-type ducks. Dietary alfalfa meal supplementation increases intestinal microbial community diversity and improves of the immune response growing egg-type ducks.

Analysis of community dynamics in environmental samples using denaturing gradient gel electrophoresis

Denaturing gradient gel electrophoresis (DGGE) is a culture-independent fingerprinting technique that allows for rapid comparative analysis of changes to microbial communities. 16S rRNA genes amplified from environmental samples can be separated based on their melting behavior in a denaturing gradient of urea and formamide. A fingerprint of the microbial community is generated with each band on the gel assumed to correspond to a different bacterial species. Community dynamics can then be assessed through statistical analysis of DGGE profiles and the sequencing of excised bands.

Biodegradation of crude oil by Pseudomonas aeruginosa and Escherichia fergusonii isolated from the Goan coast

Petroleum hydrocarbons are major pollutants of the marine environment. Bioremediation is a promising approach for treating such contaminated environments. The present study aims at isolating naturally occurring bacteria from the coast of Goa, India and to study their hydrocarbonoclastic capacity. Pseudomonas aeruginosa and Escherichia fergusonii were isolated from a crude oil-contaminated sediment sample using diesel oil as the sole carbon source. The capability of the enriched culture to degrade crude oil was estimated using microcosm studies under saline conditions. Based on GC-MS analysis, the culture was found to degrade n-alkanes at a higher rate compared to polyaromatic hydrocarbons. It was also found that the culture degraded alkylated polyaromatic hydrocarbons much less than unalkylated ones. Alkanes ranging from C12 to C33 were highly degraded compared to n-C34. This study shows bioremediation of crude oil in saline (3% NaCl) conditions by naturally existing bacteria isolated from the marine environment.

Enhanced 1,2-dichloroethane degradation in heavy metal co-contaminated wastewater undergoing biostimulation and bioaugmentation

Biostimulation, bioaugmentation and dual-bioaugmentation strategies were investigated in this study for efficient bioremediation of water co-contaminated with 1,2-dichloroethane (1,2-DCA) and heavy metals, in a microcosm set-up. 1,2-DCA concentration was periodically measured in the microcosms by gas chromatographic analysis of the headspace samples, while bacterial population and diversity were determined by standard plate count technique and Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) analysis, respectively. Dual-bioaugmentation, proved to be most effective exhibiting 22.43%, 26.54%, 19.58% and 30.49% increase in 1,2-DCA degradation in microcosms co-contaminated with As(3+), Cd(2+), Hg(2+) and Pb(2+), respectively, followed by bioaugmentation and biostimulation. Dual-bioaugmented microcosms also exhibited the highest increase in the biodegradation rate constant (k1) resulting in 1.76-, 2-, 1.7- and 2.1-fold increase in As(3+), Cd(2+), Hg(2+) and Pb(2+) co-contaminated microcosms respectively, compared to the untreated microcosms. Dominant bacterial strains obtained from the co-contaminated microcosms were found to belong to the genera Burkholderia, Pseudomonas, Bacillus, Enterobacter and Bradyrhizobium, previously reported for 1,2-DCA and other chlorinated compounds degradation. PCR-DGGE analysis revealed variation in microbial diversity over time in the different co-contaminated microcosms. Results obtained in this study have significant implications for developing innovative bioremediation strategies for treating water co-contaminated with chlorinated organics and heavy metals.

Stability of bacterial composition and activity in different salinity waters in the dynamic Patos Lagoon estuary: evidence from a lagrangian-like approach

We employed a Lagrangian-like sampling design to evaluate bacterial community composition (BCC--using temporal temperature gel gradient electrophoresis), community-level physiological profiles (CLPP--using the EcoPlate™ assay), and influencing factors in different salinity waters in the highly dynamic Patos Lagoon estuary (southern Brazil) and adjacent coastal zone. Samples were collected monthly by following limnetic-oligohaline (0-1), mesohaline (14-16), and polyhaline (28-31) waters for 1 year. The BCC was specific for each salinity range, whereas the CLPPs were similar for mesohaline and polyhaline waters, and both were different from the limnetic-oligohaline samples. The limnetic-oligohaline waters displayed an oxidation capacity for almost all organic substrates tested, whereas the mesohaline and polyhaline waters presented lower numbers of oxidized substrates, suggesting that potential activities of bacteria increased from the polyhaline to oligohaline waters. However, the polyhaline samples showed a higher utilization of some simple carbohydrates, amino acids, and polymers, indicating a shortage of inorganic nutrients (especially nitrogen) and organic substrates in coastal saltwater. The hypothesis of bacterial nitrogen limitation was corroborated by the higher Nuse index (an EcoPlate™-based nitrogen limitation indicator) in the polyhaline waters and the importance of NO(2)(-), NO(3)(-), low-molecular-weight substances, and the low-molecular-weight:high-molecular-weight substances ratio, indicated by the canonical correspondence analyses (CCAs). Our results demonstrate the important stability of microbial community composition and potential metabolic activity in the different water salinity ranges, which are independent of the region and time of the year of sample collection in the estuary. This is a quite unexpected result for a dynamic environment such as the Patos Lagoon estuary.

Risk assessment of oxytetracycline in water phase to major sediment bacterial community: a water-sediment microcosm study

With an increasing need for assessing the risk of aquaculture antibiotics, there has been growing interest in their fate and effect on sedimentary bacteria. Here we show the risk assessment for oxytetracycline (OTC) use in seawater and its subsequent transfer to sediment, and illustrate that the sediment bacterial community was stable against OTC at dosed concentrations. Water-sediment microcosm experiments were conducted to simulate quiescent aquaculture conditions. The sorption coefficient (Kd) was 12.3-44.2mL/g, which is lower than the previous reports employing vigorous mixing. In a denaturing gradient gel electrophoresis (DGGE) analysis, the addition of OTC at 50μg/L into the water phase had little effect on the major sediment bacterial community structure. This finding suggests that low concentrations of OTC in the water phase - such as those used within many aquaculture operations - do not pose a high risk of causing major changes in environmental sediment bacterial community structures.

The response of soil organism communities to the application of the insecticide lindane in terrestrial model ecosystems

The EU plant protection regulation 1107/2009/EC defines the requirements for active ingredients to be approved, specifically including the assessment of effects on biodiversity and ecosystems. According to that, semi-field methods are expected to be more important in the near future. Therefore, a higher-tier experiment suitable to assess the risk for soil organisms was conducted to further develop the TME (terrestrial model ecosystems) methodology in a dose-response design with the persistent insecticidal model compound lindane (gamma-HCH). The effects of lindane on soil communities such as collembolans, oribatid mites, nematodes, soil fungi and plant biomass were determined in 42 TME. Intact TME-soil cores (diameter 300 mm, height 400 mm) from undisturbed grassland were stored outdoor under natural climatic conditions. Lindane was applied in five concentrations between 0.032 mg active ingredients (ai)/kg dry soil and 3.2 mg ai/kg dry weight soil, six-fold replicated each. Twelve TME served as untreated controls. Abundance and community structures of oribatids, collembolans, enchytraeids, nematodes and fungi were recorded. Oribatid mites' community responded 3 months after treatment, although they were not significantly affected by the overall treatment regimen. Collembolans in total and species-specific abundance as well as the community endpoints (principal response curves, diversity measures) were adversely affected by moderate dosages of lindane. Effects were transient between 3 and 5 months after treatment with a recovery within 1 year. No significant effects could be detected for enchytraeids, nematodes and fungi. The study design and the obtained results allow for calculations of no observed effect concentrations below the highest treatment level for populations and for soil communities as defined entities, as well as effective concentrations. The paper discusses the limits of effect detection in the light of achievable coefficients of variation and by means of minimum detectable differences. Outdoor TME are useful to analyze and assess functional and structural endpoints in soil organisms' communities and their possible recovery after pesticide treatment within 1 year.

The impact of environmental heterogeneity and life stage on the hindgut microbiota of Holotrichia parallela larvae (Coleoptera: Scarabaeidae)

Gut microbiota has diverse ecological and evolutionary effects on its hosts. However, the ways in which it responds to environmental heterogeneity and host physiology remain poorly understood. To this end, we surveyed intestinal microbiota of Holotrichia parallela larvae at different instars and from different geographic regions. Bacterial 16S rRNA gene clone libraries were constructed and clones were subsequently screened by DGGE and sequenced. Firmicutes and Proteobacteria were the major phyla, and bacteria belonging to Ruminococcaceae, Lachnospiraceae, Enterobacteriaceae, Desulfovibrionaceae and Rhodocyclaceae families were commonly found in all natural populations. However, bacterial diversity (Chao1 and Shannon indices) and community structure varied across host populations, and the observed variation can be explained by soil pH, organic carbon and total nitrogen, and the climate factors (e.g., mean annual temperature) of the locations where the populations were sampled. Furthermore, increases in the species richness and diversity of gut microbiota were observed during larval growth. Bacteroidetes comprised the dominant group in the first instar; however, Firmicutes composed the majority of the hindgut microbiota during the second and third instars. Our results suggest that the gut's bacterial community changes in response to environmental heterogeneity and host's physiology, possibly to meet the host's ecological needs or physiological demands.

Coastal bacterioplankton community dynamics in response to a natural disturbance

In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of Gammaproteobacteria, Betaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition.

Influence of season and plant species on the abundance and diversity of sulfate reducing bacteria and ammonia oxidizing bacteria in constructed wetland microcosms

Constructed wetlands offer an effective means for treatment of wastewater from a variety of sources. An understanding of the microbial ecology controlling nitrogen, carbon and sulfur cycles in constructed wetlands has been identified as the greatest gap for optimizing performance of these promising treatment systems. It is suspected that operational factors such as plant types and hydraulic operation influence the subsurface wetland environment, especially redox, and that the observed variation in effluent quality is due to shifts in the microbial populations and/or their activity. This study investigated the biofilm associated sulfate reducing bacteria and ammonia oxidizing bacteria (using the dsrB and amoA genes, respectively) by examining a variety of surfaces within a model wetland (gravel, thick roots, fine roots, effluent), and the changes in activity (gene abundance) of these functional groups as influenced by plant species and season. Molecular techniques were used including quantitative PCR and denaturing gradient gel electrophoresis (DGGE), both with and without propidium monoazide (PMA) treatment. PMA treatment is a method for excluding from further analysis those cells with compromised membranes. Rigorous statistical analysis showed an interaction between the abundance of these two functional groups with the type of plant and season (p < 0.05). The richness of the sulfate reducing bacterial community, as indicated by DGGE profiles, increased in planted vs. unplanted microcosms. For ammonia oxidizing bacteria, season had the greatest impact on gene abundance and diversity (higher in summer than in winter). Overall, the primary influence of plant presence is believed to be related to root oxygen loss and its effect on rhizosphere redox.

Characterization of Freshwater Diatom Communities: Comparing Taxonomic and Genetic-Fingerprinting Approaches

Benthic diatom assemblages from five sampling sites located on two rivers were characterized simultaneously by means of traditional microscopic observations and PCR-DGGE fingerprinting with primers specifically designed for Bacillariophyceae. Community structure, richness, and diversity assessed by both methods were compared. Diatom lists obtained from morphological identification were separated into subsets, depending on (i) the taxonomic level considered (genus, species, variety) and, for each of them, (ii) the relative abundance (RA) of each component (the whole data set, RA > 1%, RA > 2%). These data were then compared to genetic fingerprinting data. Clusters based on taxonomic composition and DGGE banding patterns were very similar, showing good correspondence of community structure between the two methods. Data were compared by linear regressions between indices (richness, diversity) and by Mantel tests on dissimilarity matrices generated for each community composition data set. Statistical analysis indicated that the most reliable correlations with fingerprinting were obtained for genera representing more than 1% RA or species representing more than 2% RA. The results reveal that the PCR-DGGE protocol described here offers a satisfactory alternative for performing preliminary screening of coarse differences in diatom global community structure between samples. It can be regarded as a good complement to taxonomic analyses, which still remain necessary to detect precise changes in richness and diversity, especially when considering species with low abundance in natural assemblages.

Microbial community variation in pristine and polluted nearshore Antarctic sediments

Abstract Two molecular methods were used to investigate the microbial population of Antarctic marine sediments to determine the effects of petroleum and heavy metal pollution. Sediment samples were collected in a nested design from impacted and non-impacted locations. A detailed description of the diversity of the microbial population in two samples was obtained using 16S ribosomal DNA clone libraries constructed from an impacted and a non-impacted location. The clone libraries were very similar with the exception of two sequence clusters containing clones from only the impacted location. All samples were analysed by denaturing gradient gel electrophoresis. The band patterns generated were transformed into a presence/absence matrix and a multivariate approach was used to test for differences in the locations. Statistically significant differences were observed both between and within locations. Impacted locations showed a greater variability within themselves than the control locations. Correlations between the community patterns and environmental variables suggested that pollution was one of a number of factors affecting the microbial community composition.

Changes in human gut flora with age: an Indian familial study

Background

The gut micro flora plays vital role in health status of the host. The majority of microbes residing in the gut have a profound influence on human physiology and nutrition. Different human ethnic groups vary in genetic makeup as well as the environmental conditions they live in. The gut flora changes with genetic makeup and environmental factors and hence it is necessary to understand the composition of gut flora of different ethnic groups. Indian population is different in physiology from western population (YY paradox) and thus the gut flora in Indian population is likely to differ from the extensively studied gut flora in western population. In this study we have investigated the gut flora of two Indian families, each with three individuals belonging to successive generations and living under the same roof.

Results

Denaturation gradient gel electrophoresis analysis showed age-dependant variation in gut microflora amongst the individuals within a family. Different bacterial genera were dominant in the individual of varying age in clone library analysis. Obligate anaerobes isolated from individuals within a family showed age related differences in isolation pattern, with 27% (6 out of 22) of the isolates being potential novel species based on 16S rRNA gene sequence. In qPCR a consistent decrease in Firmicutes number and increase in Bacteroidetes number with increasing age was observed in our subjects, this pattern of change in Firmicutes / Bacteroidetes ratio with age is different than previously reported in European population.

Conclusion

There is change in gut flora with age amongst the individuals within a family. The isolation of high percent of novel bacterial species and the pattern of change in Firmicutes /Bacteroidetes ratio with age suggests that the composition of gut flora in Indian individuals may be different than the western population. Thus, further extensive study is needed to define the gut flora in Indian population.

Spatial variation of bacterial community structure of the Northern South China Sea in relation to water chemistry

Spatial distribution, diversity and composition of bacterial communities of the northern South China Sea (SCS) surface water and the relationship with the in situ environmental chemistry were investigated. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to investigate the bacterial community structure. The DGGE gel showed that each sample harbored a distinct bacterial community structure and spatial variations of bacterial community composition among all samples were obviously. A total of 17 intensive bands were excised and the sequence analysis of these DGGE bands revealed that Proteobacteria were the dominant bacterial group of surface water in the north part of SCS. Results of the taxonomic analysis showed that the communities consisted of Proteobacteria (α-subdivision, β-subdivision, γ-subdivision), Actinobacteria, Cyanobacteria, Bacteroidetes and Firmicutes. Unweighted pair group method with arithmetic averages clustering of the sampling stations indicated that all stations were classified mainly based on geographical proximity. Canonical correspondence analysis (CCA) was employed to further investigate the relationships between DGGE band pattern and the environmental variables and the first two CCA ordination axes suggested that the structure of the bacterial community was significantly correlated with the variables of nitrate (F = 1.24, P < 0.05).

Effects of the fungicide metiram in outdoor freshwater microcosms: responses of invertebrates, primary producers and microbes

The ecological impact of the dithiocarbamate fungicide metiram was studied in outdoor freshwater microcosms, consisting of 14 enclosures placed in an experimental ditch. The microcosms were treated three times (interval 7 days) with the formulated product BAS 222 28F (Polyram®). Intended metiram concentrations in the overlying water were 0, 4, 12, 36, 108 and 324 μg a.i./L. Responses of zooplankton, macroinvertebrates, phytoplankton, macrophytes, microbes and community metabolism endpoints were investigated. Dissipation half-life (DT₅₀) of metiram was approximately 1-6 h in the water column of the microcosm test system and the metabolites formed were not persistent. Multivariate analysis indicated treatment-related effects on the zooplankton (NOEC(community) = 36 μg a.i./L). Consistent treatment-related effects on the phytoplankton and macroinvertebrate communities and on the sediment microbial community could not be demonstrated or were minor. There was no evidence that metiram affected the biomass, abundance or functioning of aquatic hyphomycetes on decomposing alder leaves. The most sensitive populations in the microcosms comprised representatives of Rotifera with a NOEC of 12 μg a.i./L on isolated sampling days and a NOEC of 36 μg a.i./L on consecutive samplings. At the highest treatment-level populations of Copepoda (zooplankton) and the blue-green alga Anabaena (phytoplankton) also showed a short-term decline on consecutive sampling days (NOEC = 108 μg a.i./L). Indirect effects in the form of short-term increases in the abundance of a few macroinvertebrate and several phytoplankton taxa were also observed. The overall community and population level no-observed-effect concentration (NOEC(microcosm)) was 12-36 μg a.i./L. At higher treatment levels, including the test systems that received the highest dose, ecological recovery of affected measurement endpoints was fast (effect period < 8 weeks).

Diversity of faecal oxalate-degrading bacteria in black and white South African study groups: insights into understanding the rarity of urolithiasis in the black group

AIM

To examine whether enhanced diversity or numbers of oxalate-degrading bacteria in the gastrointestinal tracts of black South Africans play a role in determining the rarity of urolithiasis in this group.

METHODS AND RESULTS

Fresh faecal samples collected from healthy black and white South African male volunteers were analysed in terms of bacterial oxalate-degrading activity, bacterial diversity and relative species abundance. Varied bacterial populations prepared from samples from the low-risk black group showed a significantly higher level of oxalate degradation. Denaturing gradient gel electrophoresis analyses of Lactobacillus and related spp. and Bifidobacterium spp. 16S rRNA PCR products revealed a significantly higher faecal Lactobacillus diversity for the low-risk black group relative to the higher-risk white group. Quantitative real-time PCR experiments did not show any significant differences between the study groups for Lactobacillus and related spp.. However, Bifidobacterium spp. were present at a significantly higher relative abundance in the black group. Oxalobacter formigenes was present only at very low levels in either group.

CONCLUSIONS

The low abundance of O. formigenes and increased diversity and abundance of oxalate-degrading Lactobacillus and Bifidobacterium spp. in the black South African population suggest that these strains rather than O. formigenes may protect this group against calcium oxalate kidney stone disease.

SIGNIFICANCE AND IMPACT OF THE STUDY

The South African black population harbours a pool of potential oxalate-degrading lactic acid bacteria, which is more abundant and diverse than that of white South Africans. This may be useful in developing probiotics for calcium oxalate kidney stone prophylaxis.

Amplification of oral streptococcal DNA from human incisors and bite marks

Challenges to the evidentiary value of morphometric determinations have led to a requirement for scientifically substantiated approaches to the forensic analysis of bite marks. Human teeth support genotypically distinctive populations of bacteria that could be exploited for forensic purposes. This study explored the feasibility of directly amplifying bacterial DNA from bite marks for comparison with that from teeth. Samples from self-inflicted experimental bite marks (n = 24) and human incisors were amplified by PCR using primers specific for streptococcal 16S ribosomal DNA. Amplicon profiles (resolved by denaturing gradient gel electrophoresis) from bite mark samples aligned significantly more closely with profiles generated from the teeth responsible than with those from other teeth. Streptococcal amplicons were generated from dental samples applied to excised porcine skin for up to 48 h. These findings indicate that streptococcal DNA can be amplified directly from bite marks, and have potential application in bite mark analysis.

Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments

AIM

To evaluate the microbial ecology of the coronal and apical segments of infected root canal systems using a complete sampling technique and next-generation sequencing.

METHODOLOGY

The roots of 23 extracted teeth with apical periodontitis were sectioned in half, horizontally, and cryo-pulverized. Bacterial communities were profiled using tagged 454 pyrosequencing of the 16S rDNA hypervariable V5-V6 region.

RESULTS

The sequences were classified into 606 taxa (species or higher taxon), representing 24 bacterial phyla or candidate divisions and one archaeal phylum. Proteobacteria were more abundant in the apical samples (P < 0.05), whilst Actinobacteria were in significantly higher proportions in the coronal samples. The apical samples harboured statistically significantly more taxa than the coronal samples (P = 0.01) and showed a higher microbial diversity. Several taxa belonging to fastidious obligate anaerobes were significantly more abundant in the apical segments of the roots compared with their coronal counterparts.

CONCLUSIONS

Endodontic infections are more complex than reported previously. The apical part of the root canal system drives the selection of a more diverse and more anaerobic community than the coronal part. The presence of a distinct ecological niche in the apical region explains the difficulty of eradication of the infection and emphasizes the need for new treatment approaches to be developed.

Functions of effective microorganisms in bioremediation of the contaminated harbor sediments

The aim of this study was to apply loess balls containing effective microorganisms (EM) to the remediation of contaminated harbor sediments, and to thereby elucidate the functions of EM in remediation. Changes in physicochemical, biochemical, and microbiological parameters were measured to monitor the remediation process at a laboratory scale. Treatment with high concentrations of EM stock culture and EM loess balls (4%), and a low concentration of EM loess balls (0.1%) that contained molasses (0.05%) contributed to more rapid removal of malodor. Acetic acid, propionic acid, valeric acid, caponic acid, and lactic acid were rapidly removed in the presence of molasses (0.05% w/w) as a carbon nutrient source, indicating enhanced EM activity by amendment with molasses. Fermentation of molasses by EM showed that more acetic acid was produced compared with other organic acids, and that the majority of organic acids were eventually converted to acetate via intermediate metabolites. Sediment bioremediation tests showed there was no significant difference in eubacterial density with the control and the treatments. However, the density of a Lactobacillus sp. in sediments treated with 0.1% and 4.0% EM loess balls was significantly higher than the control, which indicated the bioaugmentation effect of EM loess balls in the polluted sediments. Treatment with EM loess balls and an appropriate amount of molasses, or other nutrients, will facilitate the remediation of polluted marine sediments by malodor removal, via EM degradation or utilization of offensive organic acids. To our knowledge, this is the first study to remediate contaminated marine (harbor) sediments using EM loess balls and to understand EM function during the bioaugmentation process, both in terms of organic acid metabolism and the dynamics of the engineered microbial community.