Isolates as models to study bacterial ecophysiology and biogeochemistry

Hagström, Åke; Azam, Farooq; Berg, Carlo; Zweifel, Ulla Li

doi:10.3354/ame01838

Cited by 13 publications

(14 citation statements)

References 75 publications

(80 reference statements)

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“…Bacterioplankton community composition refers to the taxonomic identity of organisms and their frequency distribution in the ecosystem. However, phenotypic identification of bacterioplankton is problematic since only a small fraction of all bacterioplankton are easily cultivable and these typically do not mirror the complete bacterioplankton diversity (Pedros-Alio, 2006;Hagström et al, 2017). Microbial ecologists therefore use culture-independent genetic identification techniques to differentiate bacterioplankton taxa (see e.g., Hugerth et al, 2015;Sunagawa et al, 2015;Beier et al, 2017;Celepli et al, 2017).…”

Section: Overview Of Baltic Sea Bacterioplankton Studiesmentioning

confidence: 99%

Sensitivity of Bacterioplankton to Environmental Disturbance: A Review of Baltic Sea Field Studies and Experiments

Lindh

Pinhassi

2018

Front. Mar. Sci.

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Bacterioplankton communities regulate energy and matter fluxes fundamental to all aquatic life. The Baltic Sea offers an outstanding ecosystem for interpreting causes and consequences of bacterioplankton community composition shifts resulting from environmental disturbance. Yet, a systematic synthesis of the composition of Baltic Sea bacterioplankton and their responses to natural or human-induced environmental perturbations is lacking. We review current research on Baltic Sea bacterioplankton dynamics in situ (48 articles) and in laboratory experiments (38 articles) carried out at a variety of spatiotemporal scales. In situ studies indicate that the salinity gradient sets the boundaries for bacterioplankton composition, whereas, regional environmental conditions at a within-basin scale, including the level of hypoxia and phytoplankton succession stages, may significantly tune the composition of bacterial communities. Also the experiments show that Baltic Sea bacteria are highly responsive to environmental conditions, with general influences of e.g. salinity, temperature and nutrients. Importantly, nine out of ten experiments that measured both bacterial community composition and some metabolic activities showed empirical support for the sensitivity scenario of bacteria-i.e., that environmental disturbance caused concomitant change in both community composition and community functioning. The lack of studies empirically testing the resilience scenario, i.e., experimental studies that incorporate the long-term temporal dimension, precludes conclusions about the potential prevalence of resilience of Baltic Sea bacterioplankton. We also outline outstanding questions emphasizing promising applications in incorporating bacterioplankton community dynamics into biogeochemical and food-web models and the lack of knowledge for deep-sea assemblages, particularly bacterioplankton structure-function relationships. This review emphasizes that bacterioplankton communities rapidly respond to natural and predicted human-induced environmental disturbance by altering their composition and metabolic activity. Unless bacterioplankton are resilient, such changes could have severe consequences for the regulation of microbial ecosystem services.

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Section: Overview Of Baltic Sea Bacterioplankton Studiesmentioning

confidence: 99%

Sensitivity of Bacterioplankton to Environmental Disturbance: A Review of Baltic Sea Field Studies and Experiments

Lindh

Pinhassi

2018

Front. Mar. Sci.

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“…Our results clearly show the distinctly different capacities of peptide utilization among the bacterial strains tested. While the current development of culture-independent techniques such as metagenomics and metatrascriptomics have advanced our knowledge of microbial ecology to a new stage, it should not detract from the attention of using model isolates to gain insights into environmental microbiomes 58 . Culture studies of single bacterial strains can particularly provide detailed physiological features of specific bacteria, an important angle to understand bacterial consortium as a whole.…”

Section: Discussionmentioning

confidence: 99%

Distinct capabilities of different Gammaproteobacterial strains on utilizing small peptides in seawater

Liu

2020

Sci Rep

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Proteins and peptides account for 20-75% of marine biota biomass, of which a major fraction is metabolized by bacteria, thus deciphering interactions between bacteria and peptides is important in understanding marine carbon and nitrogen cycling. To better understand capabilities of different bacterial strains on peptide decomposition, four Gammaproteobacteria (Pseudoalteromonas atlantica, Alteromonas sp., Marinobacterium jannaschii, Amphritea japonica) were incubated in autoclaved seawater amended with tetrapeptide alanine-valine-phenylalanine-alanine (AVFA), a fragment of RuBisCO. While AVFA was decomposed greatly by Pseudoalteromonas atlantica and Alteromonas sp, it remained nearly intact in the Marinobacterium jannaschii and Amphritea japonica incubations. Pseudoalteromonas and Alteromonas decomposed AVFA mainly through extracellular hydrolysis pathway, releasing 71-85% of the AVFA as hydrolysis products to the surrounding seawater. Overall, this study showed that Gammaproteobacterial strains differ greatly in their capabilities of metabolizing peptides physiologically, providing insights into interactions of bacteria and labile organic matter in marine environments.The microbial loop plays a significant role in shaping the temporal and spatial distributions and pathways of bioelements such as C, N, P, and Fe in seawater 1 . The microbial loop converts organic matter from dissolved to particulate phase through the buildup of microbial biomass that is further passed to higher trophic levels via grazing, thus the interaction between bacteria and dissolved organic matter (DOM) is one of the major factors determining carbon flux in the ocean 2 . Labile organic matter, such as proteins and peptides in either dissolved or particulate phases, turns over rapidly in seawater, supporting a major fraction of bacterial growth 3,4 . To be available for bacteria, proteins and peptides need to be first cleaved into small peptides (ca. <600 Da) outside cell membrane by extracellular hydrolysis 5 . Therefore, it is important to study decomposition efficiency and pathways of small peptides in order to understand C and N cycling rates and factors controlling the bacteria-DOM interactions in seawater 6-8 .Knowing "who is doing what" is a fundamental question in the field of microbial ecology, and identifying biogeochemical function of different bacteria is key to understanding their ecological niche in the environment and their contribution to biological processes. Previously, differentiating the capability of different bacteria on labile DOM decomposition is mainly based on examining the change of bacterial community structures. Copiotrophic bacteria often dominate bacterial community after labile DOM is introduced to seawater incubations 9-15 . For example, Alphaproteobacteria (including Roseobacter), Gammaproteobacteria (including Alteromonas), Flavobacteria/ Sphingobacteria, Bacteroidetes, and Verrucomicrobia can outcompete other bacterial taxa and dominate bacterial community structure in incubations after specific labile co...

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“…For example, the kinetics of a single metabolic pathway in a model 136 organism may help us understand the rate limiting steps of a narrow process, but 137 insights from model organisms are much less likely to capture the full spectrum of 138 responses of a broad process where phenotypic variation among phylogenetically 139 diverse organisms is likely to be much greater 15,16 . Defining the ecosystem process, 140 its critical sub-processes, and the known phylogenetic distribution of the metabolic 141 pathways that drive those sub-processes creates an explicit conceptual pathway that 142 links the ecosystem process to the microorganisms that contribute to it.…”

Section: Mapping Ecosystem Processes To Microbial Characteristics 110mentioning

confidence: 99%

“…Finding isolates that are 357 representative of important community properties has the potential to better 358 understand phenotypic plasticity and how constituent populations do (CATs) or do 359 not (EPs) contribute to a community property 15 . For example, work on the marine 360 bacterioplankton SAR11 has led to an increased understanding of how this 361 ubiquitous member of the marine microbiome interacts with elemental cycles in the 362 open ocean 40 .…”

Section: Applying and Testing The Proposed Framework 334mentioning

confidence: 99%

Understanding How Microbiomes Influence The Systems They Inhabit: Moving From A Correlative To A Causal Research Framework

Hall

Bernhardt

Bier

et al. 2016

Preprint

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Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

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Isolates as models to study bacterial ecophysiology and biogeochemistry

Cited by 13 publications

References 75 publications

Sensitivity of Bacterioplankton to Environmental Disturbance: A Review of Baltic Sea Field Studies and Experiments

Sensitivity of Bacterioplankton to Environmental Disturbance: A Review of Baltic Sea Field Studies and Experiments

Distinct capabilities of different Gammaproteobacterial strains on utilizing small peptides in seawater

Understanding How Microbiomes Influence The Systems They Inhabit: Moving From A Correlative To A Causal Research Framework

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