Prokaryotic abundance and 16S rRNA gene sequences detected in marine aerosols on the East Sea (Korea)

Modern studies on marine airborne prokaryotes over open seas have been rare. Here, to understand their distribution and composition, aerosol as well as surface seawater samples were collected at three sites in the East Sea. The abundance of airborne prokaryotes was 0.7-1.2 × 10(5) cells m(-3) . Partial sequences of the 16S rRNA gene from the aerosols were dominated by Gammaproteobacteria and Bacteroidetes. Interestingly, the numbers of phylotypes of airborne bacteria were comparable to those of seawater bacteria in coastal and remote offshore sites. Over half of the bacterial operational taxonomic units (OTUs) detected in these aerosols (12 out of 20) were of marine origin. Eight of the 19 bacterial OTUs found in the surface waters occurred in the aerosols. Thus, surface seawater seems to be a main source of marine airborne bacteria. However, in the intermediate offshore site, airborne bacterial OTUs (n=4) were all terrestrial, indicating that variations of dominant airborne bacterial phylotypes occurred over the sites (each ～160 km apart) sampled at 1-4-day intervals. Euryarchaeota sequences belonging to the MSP8 clade reported from geographically distant regions were detected in marine aerosols. Long-distance aerial transport of the marine prokaryotes seems to be quite possible.     

Connecting through space and time: catchment-scale distributions of bacteria in soil,stream water and sediment

Terrestrial and aquatic environments are linked through hydrological networks that transport abiotic components from upslope environments into aquatic ecosystems. However, our understanding of how bacteria are transported through these same networks is limited. Here, we applied 16S rRNA gene sequencing to over 500 soil, stream water and stream sediment samples collected within a native forest catchment to determine the extent to which bacterial communities in these habitats are connected. We provide evidence that while the bacterial communities in each habitat were significantly distinct from one another (PERMANOVA pairwise P < 0.001), the bacterial communities in soil and stream samples were weakly connected to each other when stream sediment sample locations were downhill of surface runoff flow paths. This pattern decreased with increasing distance between the soil and sediment samples. The connectivity between soil and stream water samples was less apparent and extremely transient; the greatest similarity between bacterial communities in soil and stream water overall was when comparing stream samples collected 1 week post soil sampling. This study shows how bacterial communities in soil, stream water and stream sediments are connected at small spatial scales and provides rare insights into the temporal dynamics of terrestrial and aquatic bacterial community connectivity.     

Planktonic and sediment bacterial communities in an integrated mariculture system

An integrated multi-trophic aquaculture (IMTA) system, with one fish cage model surrounded by an island and shellfish rafts, was used in the current study. Planktonic and sediment bacterial communities in the IMTA system were monitored over four seasons in 2019. In both plankton and sediment samples, the most dominant phyla were Proteobacteria and Bacteroidota. Sediment bacterial samples were more similar and had higher levels of biodiversity than planktonic bacterial samples. Obvious seasonal variations were found in plankton samples, but not in sediment samples. No obvious inter-site variations in planktonic and sediment bacteria (fish cages, shellfish rafts and control sites) were found and the results suggested that no obvious impact of feeding operations in fish culture cage model on bacterial communities in the IMTA system was observed in this study. Based on the sequence data, some faecal indicator bacteria and potentially pathogenic bacterial species were detected. According to the results, the bacterial water quality in the IMTA system was acceptable. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) analysis revealed that the primary difference in potential functional roles of planktonic and sediment bacteria was amino acid transport and metabolism, which was active in different seasons.     

Bacterial Community Composition in Central European Running Waters Examined by Temperature Gradient Gel Electrophoresis and Sequence Analysis of 16S rRNA Genes

The bacterial community composition in small streams and a river in central Germany was examined by temperature gradient gel electrophoresis (TGGE) with PCR products of 16S rRNA gene fragments and sequence analysis. Complex TGGE band patterns suggested high levels of diversity of bacterial species in all habitats of these environments. Cluster analyses demonstrated distinct differences among the communities in stream and spring water, sandy sediments, biofilms on stones, degrading leaves, and soil. The differences between stream water and sediment were more significant than those between sites within the same habitat along the stretch from the stream source to the mouth. TGGE data from an entire stream course suggest that, in the upper reach of the stream, a special suspended bacterial community is already established and changes only slightly downstream. The bacterial communities in water and sediment in an acidic headwater with a pH below 5 were highly similar to each other but deviated distinctly from the communities at the other sites. As ascertained by nucleotide sequence analysis, stream water communities were dominated by Betaproteobacteria (one-third of the total bacteria), whereas sediment communities were composed mainly of Betaproteobacteria and members of the Fibrobacteres/Acidobacteria group (each accounting for about 25% of bacteria). Sequences obtained from bacteria from water samples indicated the presence of typical cosmopolitan freshwater organisms. TGGE bands shared between stream and soil samples, as well as sequences found in bacteria from stream samples that were related to those of soil bacteria, demonstrated the occurrence of some species in both stream and soil habitats. Changes in bacterial community composition were correlated with geographic distance along a stream, but in comparisons of different streams and rivers, community composition was correlated only with environmental conditions.     

Sources of bacteria in outdoor air across cities in the midwestern United States

Bacteria are abundant in the atmosphere, where they often represent a major portion of the organic aerosols. Potential pathogens of plants and livestock are commonly dispersed through the atmosphere, and airborne bacteria can have important effects on human health as pathogens or triggers of allergic asthma and seasonal allergies. Despite their importance, the diversity and biogeography of airborne microorganisms remain poorly understood. We used high-throughput pyrosequencing to analyze bacterial communities present in the aerosol fraction containing fine particulate matter of ≤2.5 μm from 96 near-surface atmospheric samples collected from cities throughout the midwestern United States and found that the communities are surprisingly diverse and strongly affected by the season. We also directly compared the airborne communities to those found in hundreds of samples representing potential source environments. We show that, in addition to the more predictable sources (soils and leaf surfaces), fecal material, most likely dog feces, often represents an unexpected source of bacteria in the atmosphere at more urbanized locations during the winter. Airborne bacteria are clearly an important, but understudied, component of air quality that needs to be better integrated into efforts to measure and model pollutants in the atmosphere.     

Microbial diversity of eolian dust sources from saline lake sediments and biological soil crusts in arid Southern Australia

While microbial communities of aerosols have been examined, little is known about their sources. Nutrient composition and microbial communities of potential dust sources, saline lake sediments (SLS) and adjacent biological soil crusts (BSC), from Southern Australia were determined and compared with a previously analyzed dust sample. Multivariate analyses of fingerprinting profiles indicated that the bacterial communities of SLS and BSC were different, and these differences were mainly explained by salinity. Nutrient concentrations varied among the sites but could not explain the differences in microbial diversity patterns. Comparison of microbial communities with dust samples showed that deflation selects against filamentous cyanobacteria, such as the Nostocales group. This could be attributed to the firm attachment of cyanobacterial filaments to soil particles and/or because deflation occurs mainly in disturbed BSC, where cyanobacterial diversity is often low. Other bacterial groups, such as Actinobacteria and the spore-forming Firmicutes, were found in both dust and its sources. While Firmicutes-related sequences were mostly detected in the SLS bacterial communities (10% of total sequences), the actinobacterial sequences were retrieved from both (11-13%). In conclusion, the potential dust sources examined here show highly diverse bacterial communities and contain nutrients that can be transported with aerosols. The obtained fingerprinting and sequencing data may enable back tracking of dust plumes and their microorganisms.     

Dynamic changes in microbial community structure in farming pond water and their effect on the intestinal microbial community profile in juvenile common carp (Cyprinus carpio L.)

Water quality parameter dynamics, gut, sediment and water bacteria communities were studied to understand the environmental influence on the gut microbial community of a new strain of Huanghe common carp. A total of 3,384,078 raw tags and 5105 OTUs were obtained for the gut, water and sediment bacteria. The water quality had a stronger influence on the water bacteria community than gut and sediment bacteria communities. The ambient water quality parameters also significantly influenced the water and sediment bacteria communities. Comparing the gut, sediment, and water microbial communities, a relationship was found among them. However, gut bacteria were more closely related to sediment bacterial communities than to water bacteria communities. The results showed that the top three bacterial taxa were identical in gut and sediment samples in the early days of rearing. Interestingly, bacterial communities in the carp gut, water, and sediment had different adaptabilities to variations in environmental factors.     

Comparison of coliphage and bacterial aerosols at a wastewater spray irrigation site.

Microbiological aerosols were measured on a spray irrigation site at Fort Huachuca, Ariz. Indigenous bacteria and tracer bacteriophage were sampled from sprays of chlorinated and unchlorinated secondary-treatment wastewaters during day and night periods. Aerosol dispersal and downwind migration were determined. Bacterial and coliphage f2 aerosols were sampled by using Andersen viable type stacked-sieve and high-volume electrostatic precipitator samplers. Bacterial standard plate counts averaged 2.4 x 10(5) colony-forming units per ml in unchlorinated effluents. Bacterial aerosols reached 500 bacteria per m3 at 152 m downwind and 10,500 bacteria per m3 at 46m. Seeded coliphage f2 averaged 4.0 x 10(5) plaque-forming units per ml in the effluent and were detected 563 m downwind. Downwind microbial aerosol levels were somewhat enhanced by nighttime conditions. The median aerodynamic particle size of the microbial aerosols was approximately 5.0 micrometer. Chlorination reduced wastewater bacterial levels 99.97% and reduced aerosol concentrations to near background levels; coliphage f2 was reduced only 95.4% in the chlorinated effluent and was readily measured 137 m downwind. Microbiological source strength an meteorological data were used in conjunction with a dispersion model to generate mathematical predictions of aerosol strength at various sampler locations. The mean calculated survival of aerosolized bacteria (standard plate count) in the range 46 to 76 m downwind was 5.2%, and that of coliphage f2 was 4.3 %.     

Siderophore production of African dust microorganisms over Trinidad and Tobago

Iron (Fe) deposition from African dust has been implicated in a variety of environmental impacts on downwind terrestrial and marine ecosystems throughout the Caribbean. The most abundant form of Fe in African dust is Fe^III, which is often not bioavailable. The objective of this study was to determine to what degree microorganisms isolated from African dust collected in Trinidad and Tobago are capable of producing siderophores that mobilize bioavailable Fe into the environment. Aerosol samples were collected for microbial analyses during African dust conditions in the source region (Mali) and downwind sites (Trinidad and Tobago). Microbial community fingerprints, obtained by means of terminal restriction fragment length polymorphism analysis, were compared among aerosol samples and possible Trinidadian sources of locally aerosolized microorganisms (sea water and soils). Ordination of the fingerprint data revealed similarities between aerosols from the source region and the aerosols and soils of downwind regions. Aerosol isolates from the downwind sites were screened for siderophore production using a modified chrome azurol-S (CAS) assay. Twenty-five percent of isolates tested that were sampled under non-dust conditions and 65% of African dust isolates produced at least one type of siderophore; among African dust isolates, all known classes of siderophores were produced. These data support African dust microorganism siderophore production as a viable mechanism by which Fe bioavailability may be increased in downwind locations, given appropriate conditions for microbial proliferation.     

Potential pathogenic bacteria in metalworking fluids and aerosols from a machining facility

The metalworking and machining industry utilizes recirculating metalworking fluids for integral aspects of the fabrication process. Despite the use of biocides, these fluids sustain substantial biological growth. Subsequently, the high-shear forces incurred during metalworking processing aerosolize bacterial cells and may cause dermatologic and respiratory effects in exposed workers. We quantified and identified the bacterial load for metalworking fluid and aerosol samples of a machining facility in the US Midwest during two seasons. To investigate the presence of potentially pathogenic bacteria in fluid and air, we performed 16S rRNA gene surveys. The concentration of total bacterial cells (including culturable and nonculturable cells) was relatively constant throughout the study, averaging 5.1 × 10? cells mL?1 in the fluids and 4.8 × 10? cells m?3 in the aerosols. We observed bacteria of potential epidemiologic significance from several different bacterial phyla in both fluids and aerosols. Most notably, Alcaligenes faecalis was identified through both direct sequencing and culturing in every sample collected. Elucidating the bacterial community with gene surveys showed that metalworking fluids were the source of the aerosolized bacteria in this facility.     

Bacterial communities in aerosols and manure samples from two different dairies in central and Sonoma valleys of California

Aerosols have been suspected to transport food pathogens and contaminate fruits and vegetables grown in close proximity to concentrated animal feeding operations, but studies are lacking that substantiate such transport. To monitor the potential transport of bacteria originated from fresh or dry manure through aerosols on a dairy, we identified by 16S rRNA sequencing, bacteria in aerosols collected within 2 to 3 meters from dairy cows at two dairies. Gram-positive Firmicutes were predominant in aerosols from a dairy in Sonoma, California, and surrounded by vineyards, in contrast to sequences of Gram-negative Proteobacteria predominant in aerosols from a dairy in Modesto, California, also surrounded by other dairies. Although Firmicutes represented approximately 50% of the 10 most abundant sequences, aerosols from the Sonoma dairy also contained sequences of Bacteriodetes and Actinobacteria, identified previously with animal feces. While none of the top 10 sequences from fresh or dry manure from Modesto dairy were detected in aerosols, two of the sequences from the phylum Bacteriodetes and one from class Clostridia from fresh manure were detected in aerosols from Sonoma. Interestingly, none of the sequences from dry manure were in the top 10 sequences in aerosols from both dairies. The 10 most abundant sequences in aerosols from the Modesto dairy were all from Proteobacteria and nearly half of them were from genus Massilia, which have been isolated previously from immune-compromised people and aerosols. We conclude that the predominant bacteria in aerosols are diverse among locations and that they do not reflect the predominant species of bacteria present in cow feces and/or in close proximity to cows. These results suggest that the aerosol sequences did not originate from manure. Large volumes of aerosols would be required to determine if bacterial sequences from aerosols could be used to track bacteria in manure to crops grown in proximity.     

塔克拉玛干沙尘暴源区空气细菌群落多样性

【目的】采集新疆塔克拉玛干沙漠腹地和周围沙尘暴源区空气样品,对不同样点沙尘暴发生前期、中期、后期空气细菌进行群落结构解析。阐明新疆沙尘暴源区空气细菌种属特征和群落多样性动态变化规律。【方法】基于Illumina HiSeq测序平台,利用双末端测序方法,构建16S rRNA小片段文库进行测序。【结果】塔克拉玛干沙尘暴源区空气细菌主要分为4门37个属,Proteobacteria占67.6%、Bacteroidetes占17.6%、Actinobacteria占11.7%、Firmicutes占2.9%;在属水平上,新疆沙尘暴源区有8个不同优势属,非度量多维尺度分析表明,不同样点在不同时期的细菌群落组成差异极显著;典范对应分析表明,环境因子对沙尘暴源区空气细菌多样性的影响大小为:海拔纬度经度湿度气压温度,且差异不显著。【结论】新疆沙尘暴源区空气细菌群落多样性和丰富度高;不同样点沙尘暴前期、中期、后期的空气细菌群落组成差异极显著;沙尘暴对5个源区固有细菌群落影响差异极显著。     

Spatial heterogeneity in sediment-associated bacterial and eukaryotic communities in a landfill leachate-contaminated aquifer

Heterogeneity in eukaryotic and bacteria community structure in surface and subsurface sediment samples downgradient of the Banisveld landfill (The Netherlands) was studied using a culturing-independent molecular approach. Along a transect covering the part of the aquifer most polluted by landfill leachate, sediment was sampled at 1-m depth intervals, until a depth of 5.5 m, at four distances from the landfill. Two drillings were placed in a nearby clean area as a reference. Denaturing gradient gel electrophoresis banding patterns revealed high bacterial and eukaryotic diversity and complex community structures. Bacteria and eukaryotic community profiles in polluted samples grouped different from those in clean samples. Bacteria community profiles in surface samples clustered together and separately from subsurface community profiles. Subsurface bacteria profiles clustered in a location-specific manner. Eukaryotic community structure did not significantly relate to distance from the landfill or depth. No significant spatial autocorrelation of bacteria or eukaryotic communities was observed over 1-m depth intervals per sampling location. Spatial heterogeneity in sediment-associated bacterial communities appears to be much larger than in groundwater. We discuss how on the one hand, spatial heterogeneity may complicate the assessment of microbial community structure and functioning, while on the other it may provide better opportunities for natural attenuation.     

Bacterial communities in water and sediment shaped by paper mill pollution and indicated bacterial taxa in sediment in Daling River

Effluents from paper mills are highly toxic and are a major source of aquatic pollution. In this study, we collected water and sediment samples to examine the microbial communities using denaturing gradient gel electrophoresis and identified bacterial taxa greatly affected by paper mill pollution using next-generation sequencing data. Our results indicated that bacterial communities in downstream sediments were similar to those in paper mill discharge sites, indicating obvious effects of pollution, while bacterial communities in downstream water samples showed similar profiles to those in upstream sites, both being quite different from the bacterial communities in paper mill discharge sites. This was possibly because of the short contact period. In addition, bacterial communities in the estuary were quite different from those in other water and sediment samples, which was owing to the special habitat type. Considering the storage of paper mill pollutants in sediment and the significant effect on shifts in bacterial communities, we selected Clostridia and Epsilonproteobacteria at the class level and Fusibacter and Desulfobulbus at the genus level as bacterial indicators of paper mill pollution. To monitor the remediation of polluted aquatic environments, we propose Sphingobacteria, Alphaproteobacteria, Actinobacteria, Subdivision3, Planctomycetacia and Verrucomicrobiae at the class level and Bacillus, Steroidobacter, Nocardioides, Terrimonas, Pirellula and Methylibium at the genus level.     

Effect of dust and anthropogenic aerosols on columnar aerosol optical properties over Darjeeling (2200 m asl), eastern Himalayas, India

Background

The loading of atmospheric particulate matter (aerosol) in the eastern Himalaya is mainly regulated by the locally generated anthropogenic aerosols from the biomass burning and by the aerosols transported from the distance sources. These different types of aerosol loading not only affect the aerosol chemistry but also produce consequent signature on the radiative properties of aerosol.

Methodology/Principal Findings

An extensive study has been made to study the seasonal variations in aerosol components of fine and coarse mode aerosols and black carbon along with the simultaneous measurements of aerosol optical depth on clear sky days over Darjeeling, a high altitude station (2200 masl) at eastern Himalayas during the year 2008. We observed a heavy loading of fine mode dust component (Ca²⁺) during pre-monsoon (Apr – May) which was higher by 162% than its annual mean whereas during winter (Dec – Feb), the loading of anthropogenic aerosol components mainly from biomass burning (fine mode SO₄ ²⁻ and black carbon) were higher (76% for black carbon and 96% for fine mode SO₄ ²⁻) from their annual means. These high increases in dust aerosols during pre-monsoon and anthropogenic aerosols during winter enhanced the aerosol optical depth by 25 and 40%, respectively. We observed that for every 1% increase in anthropogenic aerosols, AOD increased by 0.55% during winter whereas for every 1% increase in dust aerosols, AOD increased by 0.46% during pre-monsoon.

Conclusion/Significance

The natural dust transport process (during pre-monsoon) plays as important a role in the radiation effects as the anthropogenic biomass burning (during winter) and their differential effects (rate of increase of the AOD with that of the aerosol concentration) are also very similar. This should be taken into account in proper modeling of the atmospheric environment over eastern Himalayas.     

Viability and potential for immigration of airborne bacteria from Africa that reach high mountain lakes in Europe

We have analysed the diversity of the bacteria, which grow after addition of concentrated airborne particles and desert dust in different microcosms combinations with water samples from oligotrophic alpine lakes. We used, on the one hand, airborne bacteria transported by an African dust plume and collected in a high mountain area in the central Pyrenees (Spain). On the other hand, we collected desert dust in Mauritania ( c . 3000 km distance, and a few days estimated airborne journey), a known source region for dust storms in West Africa, which originates many of the dust plumes landing on Europe. In all the dust-amended treatments we consistently observed bacterial growth of common phyla usually found in freshwater ecosystems, i.e. Alpha -, Beta - and Gammaproteobacteria , Actinobacteria , and a few Bacteroidetes , but with different composition based on lake water pretreatment and dust type. Overall, we tentatively split the bacterial community in (i) typical freshwater non-airborne bacteria, (ii) cosmopolitan long-distance airborne bacteria, (iii) non-freshwater low-distance airborne bacteria, (iv) non-freshwater long-distance airborne soil bacteria and (v) freshwater non-soil airborne bacteria. We identified viable long-distance airborne bacteria as immigrants in alpine lakes (e.g. Sphingomonas -like) but also viable putative airborne pathogens with the potential to grow in remote alpine areas ( Acinetobacter -like and Arthrobacter -like). Generation of atmospheric aerosols and remote dust deposition is a global process, largely enhanced by perturbations linked to the global change, and high mountain lakes are very convenient worldwide model systems for monitoring global-scale bacterial dispersion and pathogens entries in remote pristine environments.     

Comparison of aerosol and bioaerosol collection on air filters

Air filters efficiency is usually determined by non-biological test aerosols, such as potassium chloride particles, Arizona dust or di-ethyl-hexyl-sebacate (DEHS) oily liquid. This research was undertaken to asses, if application of non-biological aerosols reflects air filters capacity to collect particles of biological origin. The collection efficiency for non-biological aerosol was tested with the PALAS set and ISO Fine Test Dust. Flow rate during the filtration process was 720 l/h, and particles size ranged 0.246–17.165 μm. The upstream and downstream concentration of the aerosol was measured with a laser particle counter PCS-2010. Tested bioaerosol contained 4 bacterial strains of different shape and size: Micrococcus luteus, Micrococcus varians, Pseudomonas putida and Bacillus subtilis. Number of the biological particles was estimated with a culture-based method. Results obtained with bioaerosol did not confirmed 100% filters efficiency noted for the mineral test dust of the same aerodynamic diameter. Maximum efficiency tested with bacterial cells was 99.8%. Additionally, cells reemission from filters into air was also studied. Bioaerosol contained 3 bacterial strains: Micrococcus varians, Pseudomonas putida and Bacillus subtilis. It was proved that the highest intensity of the reemission process was during the first 5 min. and reached maximum 0.63% of total number of bacteria retained in filters. Spherical cells adhered stronger to the filter fibres than cylindrical ones. It was concluded that non-biological aerosol containing particles of the same shape and surface characteristics (like DEHS spherical particles) can not give representative results for all particles present in the filtered air.     

Temporal Variations in Heterotrophic Mesophilic Bacteria from a Marine Shallow Hydrothermal Vent off the Island of Vulcano (Eolian Islands, Italy)

Abstract The fluctuations of the total microbial abundance, the culturable heterotrophic bacterial population, and the composition of heterotrophic bacteria were investigated in relation to environmental parameters in a shallow, marine hydrothermal vent off the Island of Vulcano (Eolian Islands, Italy). Standing stock dynamics were studied by measuring the total population of picoplankton by direct count and the population of viable heterotrophic bacteria in water and sediment samples collected monthly. The environmental factors most strongly linked to the total microbial abundance and heterotrophic bacterial populations were pH and H₂S content in water and C/N ratio in sediment samples. The pattern of variation of microbial populations associated with water was different from those associated with sediment. Assessment of the qualitative composition of aerobic heterotrophic bacterial communities was based on 30 morphological and biochemical characteristics for each strain. Numerical analysis was used for an initial survey of the similarity among the isolates. The data were successively used to determine the structure and the metabolic potential of water and sediment bacteria. Metabolic properties varied between water- and sediment-isolated bacteria. Bacteria from water were structurally more diverse, and active in the use of carbohydrates, than those from sediment. Moreover, most of the sediment bacteria were able to grow at a high temperature (60 and 70°C). The fluctuations of bacterial characteristics in relation to environmental parameters present an evident temporal variation in water, but not in the sediment habitat. Received: 13 January 1997; Accepted: 7 August 1997     

Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis

Abstract The diversity of bacterial communities in deep marine sediments, up to 503 metres below the sea floor of the Japan Sea, was investigated by sequence analysis of amplified 16S rRNA genes. The use of different sample handling procedures greatly affected the types and diversity of sequences obtained. DNA from sediment samples stored aerobically for up to 24 h before freezing was dominated by sequences belonging to the β- and γ-proteobacteria, many of which appeared to originate from aerobic bacteria. Sub-samples equilibrated anaerobically at 16°C, were then injected with a radiotracer and immediately frozen, to simulate the conditions of a typical control sample from a radiotracer based activity assay, contained mostly α-proteobacterial sequences. Pristine sediment samples taken anaerobically and frozen within 2 h contained the widest diversity of sequences from α-, γ-, δ-proteobacteria and Gram-positive bacteria, which appeared to have originated from predominantly anaerobic or facultative bacteria. It was clear that both samples that were not frozen immediately (within 2 h) showed signs of enrichment of specific bacterial groups. Our results strongly suggest that immediate freezing should always be employed when sediment samples are to be used to assess bacterial diversity by molecular methods.     

Characterization of depth-related bacterial communities and their relationships with the environmental factors in the river sediments

To better understand the bacterial processes in river sediments, it is necessary to investigate the depth-related bacterial communities in the whole sediment profile. Sediment samples were collected to a depth of 25 cm from the Pearl River. Bacterial abundance, activity, cell-specific respiration rate, and diversity were measured, respectively, by 4′, 6-diamidino-2-phenylindole direct count, 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) staining, electron transport system by CTC reduction, and denaturing gradient gel electrophoresis analysis of 16S rRNA amplification fragments. Results showed that the bacterial metabolism activities decreased with the sediment depth. The total bacterial abundance was highest in the surface sediment with 65.1 × 10⁷ cells g⁻¹, and decreased to 11.1 × 10⁷ cells g⁻¹ below 20 cm in the sample location that suffered from heavy sewage inputs. The active bacteria accounted for 7.50–46.7% of the total bacterial number and decreased with the sediment depth. Electron transport system by the CTC reduction showed that bacterial respiration rate declined from 1.093 μmol CTC-formazan h⁻¹ g⁻¹ in the surface sediment to a half in the bottom sediment, while the cell-specific respiration increased significantly with the depth from 3.56 to 93.75 fmol CTC-formazan cell⁻¹. The bacterial diversity also changed with the depth. Beta-Proteobacteria were the dominant species in the surface sediment, whereas Delta-Proteobacteria were the main species below 10 cm. Results of canonical correspondence analysis (CCA) indicated that the distribution of bacteria was affected by the combined effect of various dissolved inorganic matter, while the respiration rate was independent of the nutrient conditions. The specific bacterial distribution contributed to not only the nutrient cycle but also enhanced pollutant decomposition in sediment of the Pearl River. The results showed that some specific bacterial species had a strong activity in the deeper layers. Therefore, the metabolic functions of the deeper bacterial species should not be neglected.