Day 3 Round-up from the Nature Conference: Environmental Microbial Biofilms and Human Microbiomes: Drivers of Future Sustainability
Tuesday, 14 February, 2017 Theme 4: Interrelation of Environmental and Human Sustainability
Background: Human (animal) health, at all scales from personal to societal, is dependent on the emergent properties of ecological communities dominated by microorganisms. Community assembly, either as part of our bodies, or in our surrounding environments, is thus central to sustainability. How communities assemble is influenced by intrinsic properties of their member species, but also by extrinsic factors such as sources of dispersing populations and dynamics of the physico-chemical environment. If we understand which environmental dimensions most strongly interact with community assembly we can improve strategies to mitigate anthropogenic influence on sustainability.
McFall-Ngai presented a different aspect of host-symbiont interactions from her keynote address in her presentation titled Dropping into the Early Conversation Between Host and symbiont: Building Tools to Understand Language. She focused on the communication processes taking place across the 100 μm span of the bob-tail squid’s light organ, and the technology that is helping to provide the answers. In particular, describing how the host is signalling to Vibrio fischeri and how the symbiont replies, using tools such as nanoSIMS, nanoString Technologies, and hybridisation chain reaction FISH.
She described how the host primes the symbiont to confer resistance to molecules (haemocyanin/cathepsin) that act as antimicrobials. As a result, V. fischeri cells in the light organ look healthy, whereas other bacteria are degrading, when viewed microscopically.
Labelled bacterial molecules (as yet described) were traced entering the host cells and being trafficked into the nucleolus and euchromatim. Colonising symbionts reside extracellularly along apical surfaces of the host epithelium, deep into the tissue, and there is a signal loss once the cells reach their destination, effectively “shutting the door behind them”.
A combination of nanoString and hybridisation chain reaction (HCR) FISH was employed to ascertain the participation of V. fischeri cells in the conversation. Single cell transcriptomics was ruled out as a method as there were too few bacterial cells.
NanoString technology uses molecular barcodes and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction. It provides high sensitivity, is easy to use and relatively cost effective with a ‘sweet spot’ of 20 to 800 transcripts. With 106 bacteria in the light organ, nanoString was 10 to 100 times more sensitive than next generation sequencing, in this study.
HCR was used to follow individual symbiont cells in deep tissue to localise the expression of transcripts and allow for the detection of low abundance transcripts in the host and symbiont.
Resolving V. fischeri biogeography during stationary phase is now a major goal to understand the nature of the host-microbe dialogue, however, the scale of the landscape remains a challenge. With a combination of these tools and further investigation, the onset of symbiosis can be viewed in real time.
Biological production in the ocean depends on phytoplankton (diatoms, dinoflagellates, cocolithophores, cyanobacteria), without which ecosystem services are lost. Sison-Mangus’s presentation on Microbial Influence on the Production of Amnesia Causing Toxin, Domoic Acid, in the Harmful Algal Bloom Forming Marine Diatom Pseudo-nitzschia covered the interactions between the toxin producing diatom and marine microbes in light of global climate change and warming oceans.
Harmful algal blooms post ecosystem wide effects, impacting organisms throughout the food web, including shellfish, fish, birds and mammals through the release of toxins such as domoic acid (DA). With warming oceans, HAB events are expected to encroach into temperate areas.
Pseudo-nitzschia was used as a model to study phytoplankton-bacteria interactions. A time series study to investigate the incidence of HAB events found that bacteria were among the factors affecting Pseudo-nitzschia blooms, along with light, salinity, nutrient availability, temperature and water flux. Here, microbes are serving an ecosystem service. In the interaction, marine bacteria depend on phytoplankton production for organic food sources, while Pseudo-nitzschia fitness is repressed in the absence of bacteria. Further, Pseudo-nitzschia loses toxin production over time when cultured axenically, and the presence of specific bacterial groups (Firmicutes, Bacteroidetes) can spike DA production. Similarly, the presence of multi-bacteria consortia can significantly spike DA production, and different combinations differentially affect the output, in vitro. In particular, members of the Bacteroidetes can rescue the growth and production of DA in bacteria-free diatom hosts, while Bacteroidetes growth is promoted in the presence of the toxin.
Data from two-year time series field sampling showed that the presence of DA is negatively correlated with bacterial diversity, with DA inhibiting growth of some bacterial groups, such as the Gamma-Proteobactera, while promoting the growth of others (Bacterioidetes, Verrucomicrobia). Conversely, Pseudo-nitzschia co-dominates with Bacteroidetes during HAB events. Overall, laboratory and field data suggest that Bacteroidetes bacteria are enhancing the production of DA by Pseudo-nitzschia in a mutualistic interaction, while inhibiting the growth of other bacteria.
In this system, the microbiome has a profound effect on diatom physiology and ecology. Diatom metabolites such as HAB toxins can structure microbiome communities, with has implications on ecosystem function and sustainability.
In her presentation on The Microbial and Ecological Signatures of Urban Water Systems, McLellan describes new indicators of faecal pollution derived from the transport of pre-treated wastewater.
The urban sewer infrastructure is a relatively new construct and totally new environment for microorganisms. McLellan’s research area encompasses the Milwaukee Sewer Service area in the US Great Lakes. Sequencing of untreated sewage found that 80% of the microbes identified did not have a faecal origin, and the pipe network throughout the city acts as a kind of chemostat. This has implications for tracing discharge from failing sewage infrastructure, especially if indicator species are not prevalent in the seepage.
Stormwater and untreated sewage from urban areas release large loads of non-indigenous bacteria into waterways, and given the majority of this is not of faecal origin, McLellan stressed the need to investigate the patterns and implications of discharge from failing sewage infrastructure.
To ascertain whether similar patterns occurred in different urban centres, McLellan’s team sampled 71 different cities across the US, collecting human faecal and pipe bacteria. Principal component analyses showed no discernible pattern for human faecal bacteria across the sample sites, but there was a strong temperature signature for pipe bacteria. Environmental organisms followed following a geographic pattern, clustering into two distinct groups based on warm and cold cities. This did not follow a steady gradient, but could be clearly delineated at the 20°C mark. Each city has a distinct and reproducible microbial community associated with its sewage distribution infrastructure.
Next generation sequencing/short reads were used to identify ecologically significant bacterial populations and develop key biomarkers to track the entry of sewage pollution into surrounding waterways. Applying these to harbour samples showed chronic sewage signals each day, which were amplified during rain events.
The ecological implications of discharging organisms selected for in an artificial chemostat into near-shore waters needs further investigation with respect to how the indigenous microbial communities are responding, and broader implications of sustainable management of urban waste.
Wilmes discusses the need to harness existing knowledge and technologies for resolving microbial community dynamics to more effectively manage microbial consortia in his presentation From Gut to Sludge: How to Sustainably Manage Microbial Communities in Future. He uses these two disparate systems to demonstrate how integrated multi-omic data can be used to design rational interventions of microbial consortia.
An integrated approach combining ‘omics data can help delineate between intrinsic and extrinsic factors contributing to microbe-host and microbial community interactions for human gut-health and wastewater microbes-environment systems. Integrated data yields more meaningful information than single components in isolation, revealing what each type of organism is actually doing.
With the appropriate toolbox, microbial systems ecology can be used to understand how different factors might affect microbial consortia, leading to shifts in community structure and function. Such shifts can have ecosystem-wide implications, especially if keystone species/functions are altered. It is important to determine the relative importance of niche and neutral processes – what aspects a niche a population can take advantage of, or what resources are available and who is accessing them.
He cites a multiple family study in Type 1 diabetes that employs an integrative approach to resolve the taxonomic and functional attributes of gut microbiota using metagenomics, metatranscriptomics and metaproteomics. Here, family membership influences the gut microbiome structure and function. Functional – but not necessarily structural – changes are key to understanding microbiome-linked disease. These approaches can be key to achieving targeted manipulation of community wide structure function relationships, with similar signatures discerned for whole pathways such as thiamine metabolism, or glycolysis, where whole networks are impacted. Such studies can provide insights into the ecosystem services provided by microbes to the host that are relevant to chronic diseases, informing on clinical focus. Similarly, for wastewater treatment an integrated ‘omics approach could identify keystone members/functions of the community that could facilitate reconstruction of community-wide networks, in a background of high perturbation and fluctuations. Assigning keystone functions were deemed more pertinent than identifying keystone genes. However, systematically resolving intrinsic and extrinsic factor associated with microbiome relationships, demonstrates that the collective functioning is more than the sum of individual components.
Holmes discussed the notion of dietary patterns supporting a sustainable and healthy host-microbiome relationship in his presentation Diversity, Cooperation and Limiting Nutrients in the Host-Microbiome Dynamic. He described alternative niche concepts, including: a niche as the sum of interactions in hyper-dimensions; the effect of niche population growth altering the environment, whereby niche destruction pertains to sustainability; and niche dimensions being fluid and subjected to evolution, conservatism and adaptive responses. The concept of ecological guilds flagged earlier in this meeting, resurfaced in Holmes’ presentation. He defined a guild as involving different organisms that occupy and interact in a similar way. Holmes used these ecological concepts to demonstrate resource dimensions from the human nutritive perspective: what our cells and tissues need to survive and thrive, and what is in our environment/how we access it. Nutritional geometry provides a platform for systematically exploring the relationship between nutrient uptake and multiple levels of the animal-microbiome system. Using this platform the microbiome could be divided into two guild based on microbial response to dietary intake: a ‘consumption type’ response (microbes that increase with intake) versus ‘limitation type’ response (those that decrease with intake). Organisms with the greatest capacity to utilise dietary nitrogen are competitively advantaged under low nutrient intake, such that the dietary complexity can be simplified according to these two response guilds. From the host perspective, the intake of protein is the greatest determiner of life span. For the holobiont, the effect of host diet has differential effects and the availability and relative proportion of particular nutrients can determine whether microbe- or host-processes drive disease or a dysbiotic state.