Open Access Kent State (OAKS)

Few studies have documented temporal changes in bacterial communities in multiple habitats in streams. In this year long study in the West Branch of the Mahoning River in Northeast Ohio, USA, bacteria in water, leaves, and sediments were examined. Bacteria were enumerated using 4,6-diamidino–2-phenylindole (DAPI) and fluorescent in situ hybridization (FISH) using taxon-specific probes for the Domain Bacteria and Burkholderia cepacia. Physical and chemical variables were also monitored. Total bacterial abundance in water (based on DAPI staining) peaked during October 2000 and July 2001; while on leaves, total abundance peaked in January then declined through April with a second June peak. The peak in sediments was during October 2000 and numbers did not differ significantly between a pool and a riffle. Domain Bacteria numbers also exhibited significant temporal changes but the seasonal patterns differed from those based on DAPI staining. Abundance of B. cepacia varied temporally on leaves but not in water and sediments. Contrary to other studies, no significant correlations were seen between bacteriological and physical/chemical variables measured. However, spring run off seems to have been a factor in temporarily reduced numbers on leaves and sediments and increasing bacterioplankton numbers, likely due to allochthonous inputs. Based on prior studies, we expected the pattern of temporal change in bacterial numbers to vary among habitats. However, there were no differences between pool and riffle sediments and no significant correlations between bacteriological and abiotic variables. This may reflect the ability of bacteria to persist under varying temperature/nutrient conditions and flow regimes. The ability of B. cepacia to maintain fairly constant populations, in contrast to the overall assemblage, likely reflects the extreme versatility of this organism.

Algal-bacterial co-variation has been frequently observed in lentic and marine environments, but the existence of such relationships in lotic ecosystems is not well established. To examine possible co-variation, bacterial number and chlorophyll-a concentration in water and sediments of nine streams from different regions in the USA were examined. In the water, a strong relationship was found between chlorophyll concentration and bacterial abundance. There was not a significant linear relationship between the abundance of sediment bacteria and sediment or water chlorophyll concentration. The linear regression results obtained between bacterial numbers and chlorophyll concentration in water were generally similar to those reported in other studies on lentic and marine systems suggesting that factors that cause this co-variation may be similar.

Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCR-denaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycete-specific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality.

Seasonal changes in the abundance of bacteria belonging to different phylogenetic groups in epilithic biofilms from a northeastern Ohio (USA) stream were examined using fluorescent in situ hybridization (FISH). Changes over a 13-mo period were observed in the biofilm assemblages, dominated by α- and β-proteobacteria. Numbers of β-proteobacteria andCytophaga–Flavobacterium peaked during the winter months and coincided with increased NO3 concentration. Actinobacteria (Gram-Positive bacteria with high guanine and cytosine [GC] content) had no relationship with any measured environmental variable and accounted for Acinetobacter calcoaceticus, Burkholderia cepacia, and Pseudomonas putida, was similar, except in the summer when numbers of B. cepacia were higher than the other 2 species. Detrended correspondence analysis extracted 2 factors that explained 69.2% of the total variation. β-proteobacteria and Cytophaga–Flavobacterium clustered with conductivity and concentrations of NO3, dissolved organic C, and soluble reactive P in the 1st factor, while A. calcoaceticus, B. cepacia, and P. putida clustered with temperature and turbidity in the 2nd factor. Our study revealed large seasonal fluctuations in the abundance of the different bacterial taxa examined in biofilms, and also demonstrated the potential influences of various environmental variables on microbial community composition in aquatic systems.

Population sizes of three bacterial species were examined in stream benthic habitats to assess differences in distribution and culturability among species. Population sizes were determined in sediments (both near bank and mid-channel) from three sites along Four Mile Creek (South Carolina, USA) using both culture-dependent (colony hybridization) and culture-independent (fluorescent in situ hybridization) techniques. The two methods used yielded different results. The numbers of colony forming units (CFU) of each species were similar in pattern to that found when the total number of CFU was enumerated (i.e., greater abundance in bank sediments and at downstream sites). In situ hybridization revealed a different distribution of these bacterial populations. Population sizes of the species were similar among sites. By using both the culture-based method and the culture-independent methods, the culturability of each species could be determined. The culturability of each species was at times much higher than the culturability of the overall assemblage. In spite of this higher culturability, viable but non-culturable cells commonly dominated the populations examined. These findings suggest that not only do bacterial species differ in population size and distribution, but also that cells within a population differ in their physiological state, or response to their environment, as reflected in differences in culturability.

Anthropogenic activities increase rates of N input to the environment, and loss of this N is controlled by several factors, including denitrification. Streams are the initial receptors of terrestrial N, but the extent to which variability in stream denitrification rates are related to differences in microbial community structure are largely unexplored. In our study, the rate of denitrification and taxonomic and functional gene diversity and abundance were examined in 3 Indiana (USA) streams with differing amounts of watershed agriculture. Taxonomic and functional gene diversity were measured using terminal restriction length polymorphisms of the 16S ribosomal ribonucleic acid (rRNA) and nitrous oxide reductase (nosZ) genes, and abundance was examined using quantitative polymerase chain reaction (Q-PCR) and total direct cell counts. As expected, streams with highest amounts of watershed agriculture had highest NO3− concentrations and highest sediment organic matter (OM) content leading to higher denitrification rates. Overall, denitrification rates were controlled primarily by sediment OM content and secondarily by nosZ abundance and nosZ terminal restriction fragment (T-RF) number. However, total bacterial numbers were not related to peaks in denitrification rate. The 2 sites with the most substantial differences in watershed agriculture, NO3− concentrations, and sediment OM content also had the largest differences in both nosZabundance and nosZ gene profiles. Overall, our results suggest that denitrification rates in agricultural streams are influenced by a combination of environmental variables (primarily benthic OM and NO3− concentrations) and microbial community composition.

Sediment bacteria are ubiquitous and important to the cycling of organic matter and nutrients in streams. We experimentally investigated the effect of sediment grain size on bacterial communities by using artificial substrata of different sizes incubated in a northeast Ohio (USA) stream. We examined abundances of specific bacterial taxa with fluorescent in situ hybridization. In general, taxon abundances were highest on 5.0-mm particles and lowest on 0.1-mm particles, and all taxa responded similarly to particle size. Few differences in abundance were found between substrata incubated in a pool or riffle in the stream or between substrata with or without organic matter amendment. Particle surface area and particle packing (sediment permeability) both affected bacterial abundance in our experiments. However, our results suggest that other factors, such as chemistry of interstitial spaces and susceptibility to predation, also contribute to differences in abundance among substrata of different particle sizes.