Bacterial diversity at surface water in three locations within the Baltic sea as revealed by culture-dependent molecular techniques

Extensive bacterial diversity indicates the potential operation of a dynamic micro-ecology within domestic rainwater storage systems

The concept that domestic rainwater storage tanks may host sustainable microbial ecosystems has not previously been addressed. The bacterial diversity, cultivated from more than 80 samples from 22 tanks at various locations across eastern Australia, is presented here as prima facie evidence for the potential operation of a functional micro-ecology within rainwater storage systems. Cultivated isolates were found to comprise members of four major bacterial divisions; Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes, including more than 200 species from 80 different genera. The pattern of abundance distribution was typical of that observed in most natural communities, comprising a small number of abundant taxa and a multitude of rare taxa, while the specific composition resembled that previously described in a number of natural aquatic systems. Although Proteobacteria from alpha, beta and gamma sub-classes were dominant, a set of core taxa comprising representative genera from all four phyla could be identified. Coliform and other species specifically associated with faecal material comprised <15% of the species identified, and represented <1.5% of total average abundance. The composition of the cultivated populations and scope of diversity present, suggested that rainwater tanks may support functional ecosystems comprising complex communities of environmental bacteria, which may have beneficial implications for the quality of harvested rainwater.

Phylogenetic and physiological diversity of bacteria isolated from Puruogangri ice core

The microbial abundance, the percentage of viable bacteria, and the diversity of bacterial isolates from different regions of a 83.45-m ice core from the Puruogangri glacier on the Tibetan Plateau (China) have been investigated. Small subunit 16S rRNA sequences and phylogenetic relationships have been studied for 108 bacterial isolates recovered under aerobic growth conditions from different regions of the ice core. The genomic fingerprints based on ERIC (enterobacterial repetitive intergenic consensus)-polymerase chain reaction and physiological heterogeneity of the closely evolutionary related bacterial strains isolated from different ice core depths were analyzed as well. The results showed that the total microbial cell, percentages of live cells, and the bacterial CFU ranged from 10(4) to 10(5) cell ml(-1) (Mean, 9.47 x 10(4); SD, 5.7 x 10(4), n = 20), 25-81%, and 0-760 cfu ml(-1), respectively. The majority of the isolates had 16S rRNA sequences similar to previously determined sequences, ranging from 92 to 99% identical to database sequences. Based on their 16S rRNA sequences, 42.6% of the isolates were high-G + C-content (HGC) gram-positive bacteria, 35.2% were low-G + C (LGC) gram-positive bacteria, 16.6% were Proteobacteria, and 5.6% were CFB group. There were clear differences in the depth distribution of the bacterial isolates. The isolates tested exhibited unique phenotypic properties and high genetic heterogeneity, which showed no clear correlation with depths of bacterial isolation. This layered distribution and high heterogeneity of bacterial isolates presumably reflect the diverse bacterial sources and the differences in bacteria inhabiting the glacier's surface under different past climate conditions.

Microbial biodiversity: approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999

Research interest in microbial biodiversity over the past 25 years has increased markedly as microbiologists have become interested in the significance of biodiversity for ecological processes and as the industrial, medical, and agricultural applications of this diversity have evolved. One major challenge for studies of microbial habitats is how to account for the diversity of extremely large and heterogeneous populations with samples that represent only a very small fraction of these populations. This review presents an analysis of the way in which the field of microbial biodiversity has exploited sampling, experimental design, and the process of hypothesis testing to meet this challenge. This review is based on a systematic analysis of 753 publications randomly sampled from the primary scientific literature from 1975 to 1999 concerning the microbial biodiversity of eight habitats related to water, soil, plants, and food. These publications illustrate a dominant and growing interest in questions concerning the effect of specific environmental factors on microbial biodiversity, the spatial and temporal heterogeneity of this biodiversity, and quantitative measures of population structure for most of the habitats covered here. Nevertheless, our analysis reveals that descriptions of sampling strategies or other information concerning the representativeness of the sample are often missing from publications, that there is very limited use of statistical tests of hypotheses, and that only a very few publications report the results of multiple independent tests of hypotheses. Examples are cited of different approaches and constraints to experimental design and hypothesis testing in studies of microbial biodiversity. To prompt a more rigorous approach to unambiguous evaluation of the impact of microbial biodiversity on ecological processes, we present guidelines for reporting information about experimental design, sampling strategies, and analyses of results in publications concerning microbial biodiversity.

Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton

The diversity of cultured planktonic bacteria was analyzed. Bacterial strains were isolated from a eutrophic lake (Zwischenahner Meer, Niedersachsen, Germany) at three different sampling dates (October 1997, April and May 1998). Phylogenetic diversity was assessed by polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and sequencing of 16S rRNA gene fragments. Enterobacterial repetitive intergenic consensus (ERIC)-PCR revealed a high genomic diversity within the strain collections, which exceeded the diversity of the 16S rRNA gene sequences considerably. The composition of each of the three strain collections was unique since strains isolated at different dates always exhibited different ERIC-PCR fingerprints. Growth tests with 59 different carbon substrates demonstrated that even strains with identical ERIC-PCR fingerprints, isolated on one sampling date, differed in their physiology. The culturable fraction investigated in the present study constituted a relatively small fraction (</=15%) of the whole bacterioplankton assemblage. Nevertheless, the high physiological diversity in this fraction already indicates that a multitude of different ecological niches must exist in the planktonic environment. The majority of strains isolated in April prior to the decay of the phytoplankton bloom were members of the Cytophaga-Flavobacterium group. One month later, not a single strain of this group could be isolated. When a group-specific PCR-DGGE technique was employed, rapid shifts in the diversity of non-cultured Cytophaga-Flavobacteria also became evident. Based on the rapid shifts in the composition of cultivated as well as some non-cultivated bacteria, the ecological niches in the planktonic habitat must undergo rapid temporal changes.

Diversity within bacterial isolates hybridizing with Comamonas probe ppT

Diversity within bacteria isolated from activated sludge and the Baltic sea and recognized by the rRNA targeted oligonucleotide probe ppT (designed by BRAUN-HOWLAND et al., 1993 to recognize C. testosteroni) was studied. The partial nucleotide sequences of 16S genes of the isolates revealed that the activated sludge and Baltic sea isolates each formed a separate group distinct from C. testosteroni. The analysis of phage and bacteriocin sensitivity as well as whole cell protein patterns revealed the same grouping, but in these characters also intragroup variation was observed. As a conclusion, neither of the studied groups were C. testosteroni, but they probably belong to two previously unknown species common in activated sludge or the Baltic sea.