Brief Background on MAGs

These MAGs provided unprecedented insights into the genomic potential of these previously unknown microbial lineages. For example, the recovered MAGs in the biofilm community revealed a self-sustaining community in terms fo carbon and nitrogen exchange. Other revelations also included the ability to identify evolutionary processes structuring the extant MAGs (Figure 1). And probably, the most important aspect of this paper was the statement: "However, even in more complex environments, it should be possible to extend the random shotgun sequencing approach to recover the genomes of uncultivated strains and species". This approach would revolutionize modern approaches to microbiomes.

Figure 1. Recovered MAG demonstrating the diversity of mosaic genome types within the Ferroplasma type II population from three closely related ancestral genome [1].

Modern Approaches and Applications

Papers:

Cellulases and leaf litter decomposition

Figure 1. Composition of leaf litter from a variety of ecosystems along an elevation gradient [1]

The top layer of soil, otherwise known as the leaf litter layer, is decaying plant debris that can be utilized by the resident microbial community. Typically, this leaf litter layer is comprised of recalcitrant, polymeric carbohydrates (Figure 1) that are difficult for bacteria to digest and incorporate into the cell. Therefore, bacteria need to release extracellular enzymes to bind to the primary source of carbohydrates and break them down to smaller byproducts before they can be used for cellular metabolism

Recently, research groups have applied some laboratory techniques to couple stable isotope probing (SIP), flow cytometry, and shotgun metagenomics. For instance, a recent paper from JGI used a "cellulose hook" (Figure 2) to recruit microbes to fluorescently labeled cellulose particles and then sorted them based on that fluorescent to sequence single cell genomes [3]. Seriously, how cool is that?! They can actually target active cellulose degraders in their system and sequence for their genomic potential. In the case of this paper, "​species-level organism with novel and phylogenetically distinct cellulolytic activity"

Fluorescent substrate strategy used to identify microbes that colonize crystalline cellulose particles [3]

Physiological trade-offs

Why invest in extracellular enzyme production if others are just going to cheat? In other words, how does the bacteria "guarantee" a return on its investment?

Main results

Outstanding questions:

Papers:

From biosynthetic genes to molecular innovation

Figure. Example of a BGC producing a molecule in a "assembly line" fashion.

To start, bacteria produce a wide variety of small molecules. Those molecules that are not required for primary metabolism were originally designated as secondary metabolites. These metabolites are produced in a modular fashion where clusters of biosynthetic genes (BGCs) interact to modify starting units derived from primary metabolism (e.g., ​Malonyl-CoA) to create these molecules (Figure).

​As a collective, the microbial genomes in each environment provide raw materials, the genomic building blocks that individuals can mix and match to create the BGCs that provide selective advantages. Adding ecological considerations to genetic and molecular studies allows the selection principles to be identified and fills out a molecule’s natural history, providing mechanistic insight into the manner in which BGCs are acquired and evolve.

Alternative models for BGC evolution

Rampant LGT of BGCs is a prevailing hypothesis in the field, but this view often overlooks the large evolutionary timescales in which an LGT event is observed. Vertical inheritance of BGCs represents an alternative mechanism. 

First, HGT is often defined very broadly and does not address criteria for what constitutes as an HGT event? Often, in natural products, BGCs are presumed to be horizontally acquired based on some homology threshold (which can be rather loose) and/or the product being detected. Furthermore, the distribution of BGCs are often reduced to a binary trait (i.e., does this strain have the BGC or not?). This can really ignore the large evolutionary timescales of these events or the amount of genetic divergence that accumulates in diverging BGCs. For instance, a patchy distribution of a BGC across strains does not equate to HGT if the BGCs have diverged in accordance with divergence time. Furthermore, the acquisition of a single genes is assumed to be a rare event, so what does that make the transfer of entire BGCs??? Loss events from extant lineages seems a more probably explanation? More to come!

Figure. Shared BGCs of Strepto. as a function of time (6).

Papers:

Using 'omics to inform biogeochemical cycles

Biogeography of nutrient-related genes

Papers:

Microbial composition and disturbances

Dormancy and Dispersal and FIRE

The authors look at both the "active" community and the total community using rRNA counts. Interestingly, there was a bottle effect in maintaining the mesocosms with a gradual decrease in richness over time (or is this a low frequency disturbance as predicted by the IDH?!). The thermal stress induced the desired effect of altering the community composition, with disturbed communities having increased beta-dispersion. Disturbed communities continued to shift through the time-course of the thermal stressor. During the recovery span, the disturbed (no dispersal) treatment remained distinct from the initial community while the dispersal treatment strongly suggests a mechanism to promote resilience and recovery (Figure). One question I had with this dispersal treatment was the huge influx of immigrants (0.5 mL of a 10% weight slurry) - this no longer functions as a passive dispersal mechanism, so I wonder how this would translate to the actual environment? Further, the results demonstrate that the dormancy provided little contribution to the recovery of the communities. Instead, opportunists and immigrants provided a means to recover.

Conclusions

Papers:

Phylosymbiosis

congruence between the evolutionary history of various host species and the community structures of their associated microbiomes

Dispersal

Selection

Selection is probably the most well-known process in structuring host-associated microbiomes; after all, the host can differentially filter microbial species pool with diet, exudates, etc. Strong evidence for the coevolution of microbiomes with hosts can be seen with phylosymbiosis in animal clades. Personally, I am a huge fan of this paper looking at the evolution of enterococci with the speciation of animals to illustrate this example [3]. By connecting bacterial genotype and phenotype to hosts, these authors found parallel speciation in enterrococci with the diversification of hosts, including the rapid speciation following the Permian Extinction (Figure) - super cool!

Ecological Drift

Diversification

Papers:

Getting from description to inference

​​1. Descriptive studies

2. Induction

The relationship between soil pH and bacterial phylotype diversity across biomes. From Fierer & Jackson. PNAS. 2006

Induction studies take descriptive studies one step further. Taking observations and making generalizations; however, these studies still lack the underlying mechanism driving these generalizations. We need to be wary of predicting off of what is known. In Prosser's article, biogeography falls into this designation where environmental parameters explain large-scale patterns. For me, the landmark biogeographic study in soil microbiomes (Figure) is a great example illustrating Prosser's point. In 2006, when the article came out, this was HUGE - a biogeographic pattern exists for microbes! [3]

3. Inference to best explanation

4. Deduction and hypothesis testing

What drives your science?

The real limitation to our understanding of microbial ecology lies, not in a lack of techniques, but in a lack of motivation, enthusiasm, desire and courage to identify and ask significant scientific questions in advance of experimental work, and a lack of testable hypotheses and theory, i.e. lack of adoption of the basic scientific method. In this respect, it is worth considering, as a microbial ecologist, if you were to be given the answer to a single scientific question, or given a theory that explained a single phenomenon, what would be your question or phenomenon; in other words, what drives your science?

Papers:

​Conceptual challenges in microbial community ecology

Microorganisms play fundamental roles in environments from the human gut to the open ocean. Since technology now allows us to catalogue the enormous diversity of microorganisms in samples, a new challenge is to interpret these data by placing them into larger conceptual frameworks. This theme issue aims to highlight new advances and potential opportunities to do that. Four overarching themes emerge from the contributions:
(1) microbial community ecology must simultaneously consider ecological and evolutionary processes,
(2) more attention should be given to interactions between microorganisms,
(3) the importance of space for microbial communities, and
​(4) the need to understand the response of microbial communities to environmental changes.

Schedule

​Before I begin, part of my break was going to Australia for some personal leave. As most people know, there are terrible fires sweeping through their national parks and other protected areas. It's estimated 1.25B animals have perished in the fires. If you can, please consider donating to the bushfire relief: wwf.org.au BONUS: photo from the trip cuddling a koala

Framework to link microbial structure to function

Phylogenetic conservatism of physiological traits. These traits will contribute to an organism's response to environmental change and, inevitably, affect the community's ability to resist change or return to its original state (resilience).

For my first post of the new year, I wanted to return to some of my favorite topics in microbial ecology: linking community patterns to function. I think it is imperative to move beyond identifying microbial community patterns and identify how various (a)biotic factors contribute to the structure of those observed patterns. For the first paper, the authors suggest employing ideas of microbial resistance and resilience to monitor microbial communities and their responses to climate [1]. These ideas were discussed over 10 years ago(!!!) by Allison & Martiny (who are two of my favorite people from my UCI time) [2]. As an aside, this paper was one of the reasons I went to UCI for my PhD - definitely a must read if you haven't already. Back to the paper at hand, the authors characterize the intrinsic (taxonomic and functional diversity) and extrinsic (both abiotic and biotic factors) that confer resistance and resilience of soil microbial communities to climate change. These connections are really only possible by applying trait-based approaches to characterize microbial life-history strategies related to climate extremes.

Quantifying physiological traits

Scaling from traits to response to whole communities

Papers: