Build your own soil: exploring microfluidics to create microbial habitat structures

Aleklett, Kristin; Kiers, E. Toby; Ohlsson, Pelle; Shimizu, Thomas S.; Caldas, Victor E.A.; Hammer, Edith C.

doi:10.1038/ismej.2017.184

Cited by 146 publications

(138 citation statements)

References 31 publications

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“…A particular challenge will also be to include the smallest spatial scales (< cm), where patchy distribution patterns of bacteria are found (Franklin and Mills, ; Cordero and Datta, ; O'Brien et al ., ; Cordero and Stocker, ). Here, small scale‐sampling devices and microsensors and innovative experimental set‐up such as microofluid devices (see, e.g., Cordero and Datta, and references therein; Aleklett et al ., ) offer promising ways ahead. In summary, we suggest that more studies should be designed to test the predictions in the conceptual model presented in Fig.…”

Section: Factors Influencing the Importance Of Different Community Asmentioning

confidence: 99%

Factors influencing aquatic and terrestrial bacterial community assembly

Langenheder

Lindström

2019

Environ Microbiol Rep

176

141

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Summary During recent years, many studies have shown that different processes including drift, environmental selection and dispersal can be important for the assembly of bacterial communities in aquatic and terrestrial ecosystems. However, we lack a conceptual overview about the ecological context and factors that influence the relative importance of the different assembly mechanisms and determine their dynamics in time and space. Focusing on free‐living, i.e., nonhost associated, bacterial communities, this minireview, therefore, summarizes and conceptualizes findings from empirical studies about how (i) environmental factors, such as environmental heterogeneity, disturbances, productivity and trophic interactions; (ii) connectivity and dispersal rates (iii) spatial scale, (iv) community properties and traits and (v) the use of taxonomic/phylogenetic or functional metrics influence the relative importance of different community assembly processes. We find that there is to‐date little consistency among studies and suggest that future studies should now address how (i)–(v) differ between habitats and organisms and how this, in turn, influences the temporal and spatial‐scale dependency of community assembly processes in microorganisms.

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Section: Factors Influencing the Importance Of Different Community Asmentioning

confidence: 99%

Factors influencing aquatic and terrestrial bacterial community assembly

Langenheder

Lindström

2019

Environ Microbiol Rep

176

141

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“…Soil is one of the most complex habitats for life on Earth (Young & Crawford, 2004;Aleklett et al, 2018). It represents a highly compact form of three-dimensionally structured habitat featuring fine-scale gradients in physico-chemical characteristics, resource availability, and gas concentrations (Young & Crawford, 2004;Bardgett, 2005).…”

Section: Soil As a Complex Habitatmentioning

confidence: 99%

“…Future studies using newer technologies (e.g. molecular techniques and visual tracking techniques) to measure movement of soil animals may help to quantify constraints on the movement of soil organisms that affect the relative importance of niche-and neutral-based processes at the microsite scale (Nunan et al, 2003;Aleklett et al, 2018). Hovatter et al (2011) showed that dispersal limitation (independent of soil environmental factors) in soil bacterial communities (i.e.…”

Section: Current Challenges and Future Directionsmentioning

confidence: 99%

Towards an integrative understanding of soil biodiversity

et al. 2019

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Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species–energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale‐dependent nature of soil biodiversity.

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“…Organizers and invited speakers highlighted ways to manipulate mycorrhizal fungal abundances in the field using fungicides and ingrowth cores (Ylva Lekberg), as well as the potential use of mutants (Thomas Irving), radioactive isotopes (Katie Field), enzymes (Bj€ orn Lindahl), and quantum dots (Victor Caldas), to study mycorrhizal function, nutrient transformation, uptake and movement. Thorunn Helgason outlined the potential use of genomic approaches, and Edith Hammer described a new technology that mimics the complexity of soils to increase realism in laboratory studies (Aleklett et al, 2018). Finally, Gaby Deckmyn reminded us all that in order to make full use of modeling, we need to collect more and better metadata (particularly environmental) during our surveys and experiments (Deckmyn et al, 2014).…”

Section: The Utility Of Existing and Emerging Technologiesmentioning

confidence: 99%

In situ mycorrhizal function – knowledge gaps and future directions

Lekberg

Helgason

2018

New Phytologist

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Summary We know a lot about the potential functions of mycorrhizas, but whether or not these are realized in the field where plants simultaneously experience a range of biotic interactions and fluctuating abiotic conditions is more or less unknown. In this Viewpoint, we present findings from a literature survey of papers on mycorrhizal function published in New Phytologist during the past 30 years. This survey showed that most functional studies are still conducted under controlled conditions, target mostly arbuscular and ectomycorrhizas, and focus on nutrient and carbon dynamics of the symbiosis. We also share discussions from a workshop, ‘In situ mycorrhizal function: how do we get relevant data from a messy world?’, held at the 9th International Conference on Mycorrhiza (ICOM9) in August 2017. In this workshop, we examined possibilities and limitations of old and new techniques for field research, and participants expressed the need to learn more about fungal traits and how they may relate to function. We argue that moving mycorrhizal experiments into the field will allow us not only to quantify realized functions, but also to revisit old paradigms and possibly discover new functions.

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Build your own soil: exploring microfluidics to create microbial habitat structures

Cited by 146 publications

References 31 publications

Factors influencing aquatic and terrestrial bacterial community assembly

Factors influencing aquatic and terrestrial bacterial community assembly

Towards an integrative understanding of soil biodiversity

In situ mycorrhizal function – knowledge gaps and future directions

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