Day 2 Round-up from the Nature Conference: Environmental Microbial Biofilms and Human Microbiomes: Drivers of Future Sustainability
Monday, 13 February, 2017 Theme 2: Molecular Microbial Ecology to Macro Ecology and Environmental Engineerng
Background: Bacteria being few cubic microns in size are driven by the ecology of life at the microscale, yet their communal activity are pivotal for all macro ecosystems both terrestrial and marine. While the experimental ecology and ecological theories are well established in both plant and animal communities, we wish to understand how this knowledge informs on microbial ecology and how an improved understanding of processes in microbial communities explains ecosystem health. These questions are also of practical importance for harnessing microbial communities in highly important environmental engineering such as water purification, wastewater bioremediation and for maintaining healthy environments.
David Wardle, Nanyang Technological University, Singapore
Wardle presented three examples of how soil microcommunities drive the aboveground plant communities in his talk: The Role of Soil Microbiota in Driving Aboveground-Belowground Linkages. At a broad scale resolution, elevation gradients in mountain regions can be proxies for anticipating effects of climate change, where the regions above and below the tree-line are indicative of particular temperature regimes. The patterns of reduced plant nutrition correlate with lower soil diversity, indicating a degree of functional redundancy in the microbial communities. At intermediate scale resolution are the shrublands in the Mediterranean type climate of Western Australia. These are global biodiversity hot-spots where plant hyperdiversity can be explained by the unique plant-microbial relationships each species harbours, together with the coexistence of other plant species and their own microbiota. The feedback between the plant, soil and microbiota results in either negative interactions where the fitness of neighbouring plants is compromised by adjacent plants, or positive interactions resulting in increased fitness of conspecifics. For fine-scale resolution, Wardle uses a system of islands in Sweden that formed from an ancient flooded valley. Here, organic soil matter has accumulated over centuries to millennia as a result of undecomposed fungal necromass and the types of fungi present determine the extent of build-up. Thus, at course resolution microbial biomass explains nutrient availability, at medium resolution, highly specific plant-microbe relationships and associations with adjacent plant-microbe units affect diversity, while at a finer resolution, plant structuring is governed by density dependent effects.
Tom Battin, Ecole Polytechnique Fédérale de Lausanne, Switzerland
In his presentation on Stream Biofilm Ecology Beyond Sequences, Battin reiterated the need to view the “theatre of activities” surrounding microbial communities and not to take a too blinkered view of narrowed components of a system. He called for approaches that are deeply rooted in ecology, to unravel the complexities of lifestyle and functional traits in highly diverse microbial communities. Complex biofilm stream communities can be dissected using amplicon sequencing to reveal biofilm populations that are relevant to ecosystem functioning, e.g. oligotrophic systems feature very different microbiomes than eutrophic systems. Core biofilm taxa act as a biofilm backbone for stream ecology. These are highly abundant and persistent in time, closely related phylogenetically and co-occur, while a subset of more stochastic taxa tends to be ephemeral.
For river systems, benthic microbial biofilms play a significant role in CO2 cycling through degradation of organic matter and phototrophic systems that coat stream sediments, with CO2 flux behaving much like a heartbeat for the stream. Given a typical stream can turn over 2 giga-tonnes per year, we need to understand stream biofilm resilience and the impact disturbances can have on ecosystem function.
Biofilm lifestyle and functional traits in streams cycle between a lag phase, high growth rate, and achieving carrying capacity, but more needs to be discerned regarding how spatial distribution affects these phases.
To understand biofilm resilience and succession we need to dissect complexity and trade-offs and “learn from each other” by taking advantage of knowledge and approaches from different disciplines.Peter Steinberg, Sydney Institute of Marine Science, University of New South Wales, Australia, Nanyang Technological University, Singapore
With the majority of the world’s population living within 60 km of the sea, understanding how to manage coastal ecosystems and resources is key to ensuring the resource is sustained. Steinberg’s presentation On Integrating Microbial Biofilms into Coastal Ecology, Management and Sustainability asked whether we can assess the relative importance of microbially mediated interactions in ecosystem engineering and health, in relation to those mediated by macro-organisms or abiotic factors.
He presented studies of natural temperate marine systems involving algal pathogens. Algae with disease phenotypes such as Kelp stipe rot or thallus bleaching feature very different microbial communities to their healthy counterparts, suggesting host wellbeing imparts a greater effect on epiphytic biofilm communities than vice versa.
The susceptibility of the host to rising sea surface temperatures was also considered. Here, microbial communities in warming oceans are implicated in causing algal disease in kelp and a red alga, and for the latter this also correspond to loss of algal defenses owing to elevated temperatures during summer. To test a possible climate change effect, experiments were conducted crossing temperature and CO2 factors, resulting in disease phenotypes for moderately increased temperatures for the interaction. However, at temperature extremes the non-disease phenotype reverts back, possibly due to a negative effect of temperature on the pathogens themselves.
Coincidently, the tropicalisation of temperate coastal waters from a southward shift of the warm East Australia Current has resulted in a 10-fold increase in tropical herbivorous fish in temperate seaweed communities since 2002. Such shifts are occurring in western boundary currents worldwide and are leading to increased herbivory of algae-dominated systems. Phenomena such as these flip the conversation and call for a better understand of the bigger picture, if we are to assess the relative importance of microbial versus macrobial/environmental factors.
The sustainability and management of coastal systems is viewed by policy makers in broad terms, such as alleviating threats to ecosystems (e.g. Great Barrier Reef) or coastal infrastructure and development. We need to understand where microbes stand in the considerations of coastal management and ensure policy makers are kept well informed of the integral role microbial communities play in ecosystem engineering.
Kenneth Nealson, University of Southern California, USA
Nealson’s presentation on Extracellular Electron Transfer (EET): Opening New Windows of Metabolic Opportunity opens up the consideration that surface potential is an important aspect of microbial ecology, especially in biofilms.
Old-school assays using neutral glass plates as substrates for biofilm colonisation neglected the fact that many surfaces in nature are electrically charged (either positively or negatively). While the effect of surface potential on biofilm behaviour might not have formed the basis of experimental focus, the neutral charge of glass might result in different outcomes than more ecologically relevant surfaces that have electrons flowing through the biofilm to the surface and vice versa. The discovery three decades ago that bacteria respond to changes in surface potential has opened up a new line of investigation into the metabolic possibilities of microbial biofilms. This is a concept biofilm researchers need to consider.
Electrochemically active bacteria (those capable of EET) were identified when metal reduction was observed to occur too fast for it to be chemically driven. The conclusion was there must be a microbial component driving the reduction, and Shewanella oneidensis was implicated via anaerobic respiration, dispelling the belief that organisms were not capable of utilising a solid for respiration.
In a compelling example of convergent evolution, Geobacter sp. have also evolved the machinery for EET, but achieve the same end using very different multi-haeme c-type cytochromes to move electrons from the periplasm to the cell exterior.
These are highly adapted and selected for systems that are being utilised as microbial fuel cells and other bioelectrochemical devices. Conversely, the electrodes used in these fuel cells have attracted novel microbes, with the emergence of new strains of previously unculturable (via traditional methods) bacteria now a common occurrence. The existence of EET microbes is more widespread than initially thought, and they perform better in mixed culture compared to single species biofilms.
Studies of electrochemically active systems have taught us that: bacteria prefer charged surfaces, and different communities/strains prefer different charge conditions; many previously uncultivated microbes have been isolated using electron acceptors/donors in various biofilm communities; many of the new microbes are already known to us, but have not been well examined; and bacteria can sense and respond to changes in electrical potential.
Marilyn Roossinck, Stanford University School of Medicine, USA
Roossinck’s discussion of Viruses in the Phytobiome: Abundance and Ecological Roles gives viruses a positive spin to counter the bad publicity they normally receive. As with bacteria, the majority of viruses are not pathogenic but form persistent associations with their hosts.
The field of virology had adopted a reductionist viewpoint until a decade ago, predominantly concentrating on human-related viruses. That all changed with technical advances that allowed virus ecologists to view the broader picture and investigate viruses in wild hosts.
Roossinck’s research focuses on plant viruses, the vast majority of which are persistent, having long relationships with their hosts and close to 100% vertical transmission. Although the majority of relationships between plants and viruses are mutualistic, the associations span a spectrum of symbioses to mutualistic to commensal to antagonistic.
Mutualistic interactions include viruses imparting thermo-tolerance or draught tolerance to the host plants, increased germination rates, and protecting the plant from acute infections. Roossinck’s review of virus-host interactions helps to dispel some of the negative press (see review: Roossinck (2015) J. Virol. 89: 6532–6535).
Ehud Banin, Bar-Ilan University, Ramat-Gan, Israel
In a post-antibiotic era there is increased pressure to develop alternative means to eradicate or control biofilms in an effective and sustainable way for medical, agricultural and industrial systems. Banin explains some novel solutions to the problem of biofouling in his presentation Biofouling – Can we do something about it?
Biofilm formation is the precursor to biofouling and can therefore be targeted in the control of the latter. Antibiofilm strategies typically focus on the various stages in the biofilm lifecycle, from adhesion, through biofilm growth and dispersion. Here, Banin presents as strategy of preventing biofilm adhesion on catheters by employing acoustic waves to deter biofilm formation and delay the onset of catheter associated infections. Another ‘Trojan Horse’ strategy gains access to bacterial cells using the element gallium disguised as iron, which is taken up via bacterial siderophores and subsequently interferes with bacterial iron metabolism. A third, non-clinical approach uses a novel antibiofilm self-cleaning irrigation dripper containing rechargeable N-halamine nanoparticles that deter biofilm formation, which disrupts the distribution of water along the irrigation hoses. In a plus for sustainability, the nanoparticles can be easily and safely recharged with halides by flushing with a weak bleach solution, restoring months of efficacy.