scholarly journals Characterizing the Uncultivated Microbial Minority: towards Understanding the Roles of the Rare Biosphere in Microbial Communities

mSystems ◽  
2021 ◽  
Author(s):  
Jimmy H. W. Saw

Microbial communities are frequently numerically dominated by just a few species. Often, the long “tail” of the rank-abundance plots of microbial communities constitutes the so-called “rare biosphere,” microorganisms that are highly diverse but are typically found in low abundance in these communities.

PLoS ONE ◽  
2012 ◽  
Vol 7 (1) ◽  
pp. e29973 ◽  
Author(s):  
Juan M. Gonzalez ◽  
Maria C. Portillo ◽  
Pedro Belda-Ferre ◽  
Alex Mira

2019 ◽  
Vol 85 (10) ◽  
Author(s):  
Lars Schreiber ◽  
Nathalie Fortin ◽  
Julien Tremblay ◽  
Jessica Wasserscheid ◽  
Miria Elias ◽  
...  

ABSTRACTWestern Canada produces large amounts of bitumen, a heavy, highly weathered crude oil. Douglas Channel and Hecate Strait on the coast of British Columbia are two water bodies that may be impacted by a proposed pipeline and marine shipping route for diluted bitumen (dilbit). This study investigated the potential of microbial communities from these waters to mitigate the impacts of a potential dilbit spill. Microcosm experiments were set up with water samples representing different seasons, years, sampling stations, and dilbit blends. While the alkane fraction of the tested dilbit blends was almost completely degraded after 28 days, the majority of the polycyclic aromatic hydrocarbons (PAHs) remained. The addition of the dispersant Corexit 9500A most often had either no effect or an enhancing effect on dilbit degradation. Dilbit-degrading microbial communities were highly variable between seasons, years, and stations, with dilbit type having little impact on community trajectories. Potential oil-degrading genera showed a clear succession pattern and were for the most part recruited from the “rare biosphere.” At the community level, dispersant appeared to stimulate an accelerated enrichment of genera typically associated with hydrocarbon degradation, even in dilbit-free controls. This suggests that dispersant-induced growth of hydrocarbon degraders (and not only increased bioavailability of oil-associated hydrocarbons) contributes to the degradation-enhancing effect previously reported for Corexit 9500A.IMPORTANCEWestern Canada hosts large petroleum deposits, which ultimately enter the market in the form of dilbit. Tanker-based shipping represents the primary means to transport dilbit to international markets. With anticipated increases in production to meet global energy needs, the risk of a dilbit spill is expected to increase. This study investigated the potential of microbial communities naturally present in the waters of a potential dilbit shipping lane to mitigate the effects of a spill. Here we show that microbial degradation of dilbit was mostly limited ton-alkanes, while the overall concentration of polycyclic aromatic hydrocarbons, which represent the most toxic fraction of dilbit, decreased only slightly within the time frame of our experiments. We further investigated the effect of the oil dispersant Corexit 9500A on microbial dilbit degradation. Our results highlight the fact that dispersant-associated growth stimulation, and not only increased bioavailability of hydrocarbons and inhibition of specific genera, contributes to the overall effect of dispersant addition.


Geosciences ◽  
2018 ◽  
Vol 8 (11) ◽  
pp. 418 ◽  
Author(s):  
Maija Nuppunen-Puputti ◽  
Lotta Purkamo ◽  
Riikka Kietäväinen ◽  
Mari Nyyssönen ◽  
Merja Itävaara ◽  
...  

The deep biosphere contains a large portion of the total microbial communities on Earth, but little is known about the carbon sources that support deep life. In this study, we used Stable Isotope Probing (SIP) and high throughput amplicon sequencing to identify the acetate assimilating microbial communities at 2260 m depth in the bedrock of Outokumpu, Finland. The long-term and short-term effects of acetate on the microbial communities were assessed by DNA-targeted SIP and RNA targeted cell activation. The microbial communities reacted within hours to the amended acetate. Archaeal taxa representing the rare biosphere at 2260 m depth were identified and linked to the cycling of acetate, and were shown to have an impact on the functions and activity of the microbial communities in general through small key carbon compounds. The major archaeal lineages identified to assimilate acetate and metabolites derived from the labelled acetate were Methanosarcina spp., Methanococcus spp., Methanolobus spp., and unclassified Methanosarcinaceae. These archaea have previously been detected in the Outokumpu deep subsurface as minor groups. Nevertheless, their involvement in the assimilation of acetate and secretion of metabolites derived from acetate indicated an important role in the supporting of the whole community in the deep subsurface, where carbon sources are limited.


2016 ◽  
Author(s):  
Nuria Fernandez-Gonzalez ◽  
Julie A. Huber ◽  
Joseph J. Vallino

AbstractAlthough microbial systems are well-suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20 day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function was used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appear inherently well-adapted to disturbances in energy input and that changes in community structure in both treatments are more dependent on internal dynamics than on external forcing. Results also show that the rare biosphere is critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, endogenous feedbacks were more important than exogenous drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics.IMPORTANCEWithin the broader ecological context, biological communities are often viewed as stable and only experience succession or replacement when subject to external perturbations, such as changes in food availability or introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic ”unstable” communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems.


Author(s):  
J. J. Laidler

The presence of three-dimensional voids in quenched metals has long been suspected, and voids have indeed been observed directly in a number of metals. These include aluminum, platinum, and copper, silver and gold. Attempts at the production of observable quenched-in defects in nickel have been generally unsuccessful, so the present work was initiated in order to establish the conditions under which such defects may be formed.Electron beam zone-melted polycrystalline nickel foils, 99.997% pure, were quenched from 1420°C in an evacuated chamber into a bath containing a silicone diffusion pump fluid . The pressure in the chamber at the quenching temperature was less than 10-5 Torr . With an oil quench such as this, the cooling rate is approximately 5,000°C/second above 400°C; below 400°C, the cooling curve has a long tail. Therefore, the quenched specimens are aged in place for several seconds at a temperature which continuously approaches the ambient temperature of the system.


2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.


Pneumologie ◽  
2009 ◽  
Vol 63 (S 01) ◽  
Author(s):  
T Zakharkina ◽  
C Herr ◽  
A Yildirim ◽  
M Friedrich ◽  
R Bals

Planta Medica ◽  
2015 ◽  
Vol 81 (11) ◽  
Author(s):  
JJ Araya ◽  
M Chavarría ◽  
A Pinto-Tomás ◽  
C Murillo ◽  
L Uribe ◽  
...  

2018 ◽  
Author(s):  
L van Uden ◽  
G Seliger ◽  
M Bergner ◽  
M Entezami ◽  
M Tchirikov
Keyword(s):  

2016 ◽  
Vol 552 ◽  
pp. 93-113 ◽  
Author(s):  
AT Davidson ◽  
J McKinlay ◽  
K Westwood ◽  
PG Thomson ◽  
R van den Enden ◽  
...  

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