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(searched for: pmid:5011884)
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Seth A. Steichen, Song Gao, Peter Waller,
Published: 25 May 2020
Microbial Biotechnology, Volume 13, pp 1546-1561; https://doi.org/10.1111/1751-7915.13591

Abstract:
Microalgae as a biofuel source are of great interest. Bacterial phycosphere inhabitants of algal cultures are hypothesized to contribute to productivity. In this study, the bacterial composition of the Chlorella sorokiniana phycosphere was determined over several production cycles in different growing seasons by 16S rRNA gene sequencing and identification. The diversity of the phycosphere increased with time during each individual reactor run, based on Faith’s phylogenetic diversity metric versus days post-inoculation (R = 0.66, P < 0.001). During summer months, Vampirovibrio chlorellavorus, an obligate predatory bacterium, was prevalent. Bacterial sequences assigned to the Rhizobiales, Betaproteobacteriales and Chitinophagales were positively associated with algal biomass productivity. Applications of the general biocide, benzalkonium chloride, to a subset of experiments intended to abate V. chlorellavorus appeared to temporarily suppress phycosphere bacterial growth, however, there was no relationship between those bacterial taxa suppressed by benzalkonium chloride and their association with algal productivity, based on multinomial model correlations. Algal health was approximated using a model-based metric, or the ‘Health Index’ that indicated a robust, positive relationship between C. sorokiniana fitness and presence of members belonging to the Burholderiaceae and Allorhizobium–Neorhizobium–Pararhizobium–Rhizobium clade. Bacterial community composition was linked to the efficiency of microalgal biomass production and algal health.
Pallavi P. Murugkar, Andrew J. Collins, Tsute Chen,
Published: 1 January 2020
Journal of Oral Microbiology, Volume 12; https://doi.org/10.1080/20002297.2020.1814666

Abstract:
The vast majority of bacteria on earth have not yet been cultivated. There are many bacterial phyla with no cultivated examples including most members of the Candidate Phylum Radiation with the exception of human oral isolates from the phylum Saccharibacteria. The aims of this research were to develop reproducible methods and validate approaches for the cultivation of human oral Saccharibacteria and to identify the conceptual pitfalls that delayed isolation of these bacteria for 20 years after their discovery. Oral samples were dispersed and passed through 0.2 µm membrane filters. The ultrasmall saccharibacterial cells in the filtrate were pelleted, inoculated into broth cultures of potential bacterial host cells and passaged into fresh medium every 2–3 days. Thirty-two isolates representing four species of Saccharibacteria were isolated in stable coculture with three species of host bacteria from the phylum Actinobacteria. Complete genome sequences were obtained for 16 isolates. Human oral Saccharibacteria are obligate bacterial parasites that can be stably passaged in coculture with specific species of host bacteria. Isolating these important members of the human oral microbiome, and many natural environments, requires abandoning many of Koch’s concepts and methods and embracing novel microbiological approaches.
Published: 14 January 2019
Frontiers in Microbiology, Volume 9; https://doi.org/10.3389/fmicb.2018.03344

Abstract:
The phylum Cyanobacteria comprises a non-photosynthetic lineage. The diversity and distribution of non-photosynthetic cyanobacteria (NCY) across aquatic environments are currently unknown, including their ecology. Here, we report about composition and phylogenetic diversity of two clades of NCY in ten lakes of the European peri-Alpine region, over the past ∼100 years. Using 16S rDNA sequences obtained from dated sediment cores, we found almost equal proportion of taxa assigned to Melainabacteria and the deepest-branching group Sericytochromatia (ML635J-21) (63 total detected taxa). The topology of our reconstructed phylogenies reflected evolutionary relationships expected from previous work, that is, a clear separation between the deepest branching Sericytochromatia, the Melainabacteria, and the photosynthetic cyanobacteria clades. While different lakes harbored distinct NCY communities, the diversity of NCY assemblages within and between lakes (alpha and beta diversity) did not significantly change over the last century. This is in contrast with what was previously reported for photosynthetic cyanobacteria. Unchanged community phylogenetic similarity over geographic distance indicated no dispersal limitation of NCY at the regional scale. Our results solicit studies linking in-lake environmental factors to the composition of these microorganisms’ communities, whose assembly appeared not to have been influenced by large-scale anthropogenic environmental changes. This is the first attempt to study the diversity and distribution of NCY taxa across temperate lakes. It provides a first step towards understanding their distribution and ecological function in pelagic aquatic habitats, where these organisms seem to be prevalent.
, Johanna Schmidt, Ulrike Koll, Manfred Rohde, Susanne Verbarg, , Ryosuke Nakai, Takeshi Naganuma, Elke Lang
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Volume 67, pp 2555-2568; https://doi.org/10.1099/ijsem.0.001965

Abstract:
The unusual chemo-organoheterotrophic proteobacterial strain MWH-Nonnen-W8redT was isolated from a lake located in the Black Forest (Schwarzwald), Germany, by using the filtration-acclimatization method. Phylogenetic analyses based on the 16S rRNA gene sequence of the strain could not provide clear hints on classification of the strain in one of the current classes of the phylum Proteobacteria . Whole-genome sequencing resulted in a genome size of 3.5 Mbp and revealed a quite low DNA G+C content of 32.6 mol%. In-depth phylogenetic analyses based on alignments of 74 protein sequences of a phylogenetically broad range of taxa suggested assignment of the strain to a new order of the class Oligoflexia . These analyses also suggested that the order Bdellovibrionales should be transferred from the class Deltaproteobacteria to the class Oligoflexia , that this order should be split into two orders, and that the family Pseudobacteriovoracaceae should be transferred from the order Bdellovibrionales to the order Oligoflexales . We propose to establish for strain MWH-Nonnen-W8redT (=DSM 23856T=CCUG 58639T) the novel species and genus Silvanigrella aquatica gen. nov., sp. nov. to be placed in the new family Silvanigrellaceae fam. nov. of the new order Silvanigrellales ord. nov.
, Charles E. Sellers, Braden W. Bennett, Eric M. Lyons, Laura T. Carney
Published: 20 June 2016
Frontiers in Microbiology, Volume 7; https://doi.org/10.3389/fmicb.2016.00848

Abstract:
The predatory bacterium, Vampirovibrio chlorellavorus, can destroy a Chlorella culture in just a few days, rendering an otherwise robust algal crop into a discolored suspension of empty cells. Chlorella is used as a benchmark for open pond cultivation due to its fast growth. In nature, V. chlorellavorus plays an ecological role by controlling this widespread terrestrial and freshwater microalga, but it can have devastating effects when it attacks large commercial ponds. We discovered that V. chlorellavorus was associated with the collapse of four pilot commercial-scale (130,000 L) open-pond reactors. Routine microscopy revealed the distinctive pattern of V. chlorellavorus attachment to the algal cells, followed by algal cell clumping, culture discoloration and ultimately, growth decline. The "crash" of the algal culture coincided with increasing proportions of 16s rRNA sequencing reads assigned to V. chlorellavorus. We designed a qPCR assay to anticipate an impending culture crash and developed a novel treatment to control the bacterium. We found that 1) Chlorella growth was not affected by a 15 min exposure to pH 3.5 in the presence of 0.5 g/L acetate, when titrated with hydrochloric acid and 2) this treatment had a bactericidal effect on the culture (2-log decrease in aerobic counts). Therefore, when qPCR results indicated a rise in V. chlorellavorus amplicons, we found that the pH-shock treatment prevented the crash and doubled the productive longevity of the culture. Furthermore, the treatment could be repeatedly applied to the same culture, at the beginning of at least two sequential batch cycles. In this case, the treatment was applied preventively, further increasing the longevity of the open pond culture. In summary, the treatment reversed the infection of V. chlorellavorus as confirmed by observations of bacterial attachment to Chlorella cells and by detection of V. chlorellavorus by 16s rRNA sequencing and qPCR assay. The pH-shock treatment is highly selective against prokaryotes, and it is a cost-effective treatment that can be used throughout the scale up and production process. To our knowledge, the treatment described here is the first effective control of V. chlorellavorus and will be an important tool for the microalgal industry and biofuel research.
Charles Pepe-Ranney, Ashley N. Campbell, Chantal N. Koechli, Sean Berthrong,
Published: 12 May 2016
Frontiers in Microbiology, Volume 7; https://doi.org/10.3389/fmicb.2016.00703

Abstract:
We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi and Planctomycetes.
Guanghong Zuo, Xiaoyang Zhi, Zhao Xu,
Published: 25 March 2016
Genomics, proteomics & bioinformatics, Volume 14, pp 94-102; https://doi.org/10.1016/j.gpb.2015.12.002

Abstract:
We describe an interactive viewer for the All-Species Living Tree (LVTree). The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner. In view of the fact that the present prokaryotic systematics is largely based on 16S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla (Proteobacteria and Firmicutes) to monophyletic clusters.
Published: 21 May 2015
Journal: PeerJ
Abstract:
An uncultured non-photosynthetic basal lineage of the Cyanobacteria, the Melainabacteria, was recently characterised by metagenomic analyses of aphotic environmental samples. However, a predatory bacterium, Vampirovibrio chlorellavorus, originally described in 1972 appears to be the first cultured representative of the Melainabacteria based on a 16S rRNA sequence recovered from a lyophilised co-culture of the organism. Here, we sequenced the genome of V. chlorellavorus directly from 36 year-old lyophilised material that could not be resuscitated confirming its identity as a member of the Melainabacteria. We identified attributes in the genome that likely allow V. chlorellavorus to function as an obligate predator of the microalga Chlorella vulgaris, and predict that it is the first described predator to use an Agrobacterium tumefaciens-like conjugative type IV secretion system to invade its host. V. chlorellavorus is the first cyanobacterium recognised to have a predatory lifestyle and further supports the assertion that Melainabacteria are non-photosynthetic.
, , Isabel Esteve, , David Chase, Lynn Margulis
Proceedings of the National Academy of Sciences of the United States of America, Volume 83, pp 2138-2142; https://doi.org/10.1073/pnas.83.7.2138

Abstract:
Two kinds of predatory bacteria have been observed and characterized by light and electron microscopy in samples from freshwater sulfurous lakes in northeastern Spain. The first bacterium, named Vampirococcus , is Gram-negative and ovoidal (0.6 μm wide). An anaerobic epibiont, it adheres to the surface of phototrophic bacteria ( Chromatium spp.) by specific attachment structures and, as it grows and divides by fission, destroys its prey. An important in situ predatory role can be inferred for Vampirococcus from direct counts in natural samples. The second bacterium, named Daptobacter , is a Gram-negative, facultatively anaerobic straight rod (0.5 × 1.5 μm) with a single polar flagellum, which collides, penetrates, and grows inside the cytoplasm of its prey (several genera of Chromatiaceae). Considering also the well-known case of Bdellovibrio , a Gram-negative, aerobic curved rod that penetrates and divides in the periplasmic space of many chemotrophic Gram-negative bacteria, there are three types of predatory prokaryotes presently known (epibiotic, cytoplasmic, and periplasmic). Thus, we conclude that antagonistic relationships such as primary consumption, predation, and scavenging had already evolved in microbial ecosystems prior to the appearance of eukaryotes. Furthermore, because they represent methods by which prokaryotes can penetrate other prokaryotes in the absence of phagocytosis, these associations can be considered preadaptations for the origin of intracellular organelles.
I. Estève, , , C. Abellà
Published: 1 April 1983
Microbial Ecology, Volume 9, pp 57-64; https://doi.org/10.1007/bf02011580

Abstract:
Epibiontic cells on the surface of the photosynthetic purple sulfur bacteriumChromatium minus, collected several times during the year from 3 different Spanish lakes, were examined using scanning and transmission electron microscopy. The cells attached to theC. minus cell wall by an electron-dense pad, but did not enter the cell. They were ovoidal (about 0.6Μm wide) when free, and slightly curved rods (0.3×0.6Μm) when undergoing division. Division only occurred when cells remained attached toChromatium. A septum was formed, resulting in 2 or 3 curved rods surrounded by a common capsule. Detached daughter cells became ovoidal. The host ultrastructure changed as a result of epibiontic attachment, showing symptoms of cellular degradation. Simultaneously, plaques could be detected on cell lawns formed spontaneously upon cell sedimentation from field samples.
Douglas L. McBride, Paul Kugrens, John A. West
Published: 1 September 1974
Journal: Protoplasma
Protoplasma, Volume 79, pp 249-264; https://doi.org/10.1007/bf01276605

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