Quantitatively Partitioning of microbial function among taxonomic ranks across the tree of life

Widely used microbial taxonomies, such as the NCBI taxonomy, are based on a combination of sequence homology among conserved genes and historically accepted taxonomies, which were developed based on observable traits such as morphology and physiology. A recently proposed alternative taxonomy database, the Genome Taxonomy Database (GTDB), incorporates only sequence homology of conserved genes and attempts to partition taxonomic ranks such that each rank implies the same amount of evolutionary distance, regardless of its position on the phylogenetic tree. This provides the first opportunity to completely separate taxonomy from traits and therefore to quantify how taxonomic rank corresponds to traits across the microbial tree of life. We quantified the relative abundances of clusters of orthologous group functional categories (COG-FCs) as a proxy for traits within the lineages of 13,735 cultured and uncultured microbial lineages from a custom-curated genome database. On average, 41.4% of the variation in COG-FC relative abundance is explained by taxonomic rank, with domain, phylum, class, order, family, and genus explaining, on average, 3.2%, 14.6%, 4.1%, 9.2%, 4.8%, and 5.5% of the variance, respectively (P \u3c 0.001 for all). To our knowledge, this is the first work to quantify the variance in metabolic potential contributed by individual taxonomic ranks. A qualitative comparison between the COG-FC relative abundances and genus-level phylogenies, generated from published concatenated protein sequence alignments, further supports the idea that metabolic potential is taxonomically coherent at higher taxonomic ranks. The quantitative analyses presented here characterize the integral relationship between diversification of microbial lineages and the metabolisms which they host

Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes

We applied theoretical and simulation-based approaches to characterize how microbial community structure influences the amount of sequencing effort to reconstruct metagenomes that are assembled from short-read sequences. First, a coupon collector equation was proposed as an analytical model for predicting sequencing effort as a function of microbial community structure. Characterization was performed by varying community structure properties such as richness, evenness, and genome size. Simulations demonstrated that while community richness and evenness influenced the sequencing effort required to sequence a community metagenome to exhaustion, the effort necessary to sequence an individual genome to a target fraction of exhaustion depended only on the relative abundance of the genome and its genome size. A second analysis evaluated the quantity, completion, and contamination of metagenome-assembled genomes (MAGs) as a function of sequencing effort on four preexisting sequence read data sets from different environments. These data sets were subsampled to various degrees of completeness to simulate the effect of sequencing effort on MAG retrieval. Modeling suggested that sequencing efforts beyond what is typical in published experiments (1 to 10 Gbp) would generate diminishing returns in terms of MAG binning. A software tool, Genome Relative Abundance to Sequencing Effort (GRASE), was created to assist investigators to further explore this relationship. Reevaluation of the relationship between sequencing effort and binning success in the context of genome relative abundance, as opposed to base pairs, provides a constraint on sequencing experiments based on the relative abundance of microbes in an environment rather than arbitrary levels of sequencing effort. IMPORTANCE Short-read sequencing with Illumina sequencing technology provides an accurate, high-throughput method for characterizing the metabolic potential of microbial communities. Short-read sequences can be assembled and binned into metagenome-assembled genomes, thus shedding light on the function of microbial ecosystems that are important for health, agriculture, and Earth system processes. The work presented here provides an analytical framework for selecting sequencing effort as a function of genome relative abundance. As such, experimental goals in metagenome-assembled genome creation projects can select sequencing effort based on the rarest target genome as a constrained threshold. We hope that the results presented here, as well as GRASE, will be valuable to researchers planning sequencing experiments

Microbial degradation of organic macromolecules in Arctic fjords and in the Gulf of Mexico

Polysaccharides represent a labile, abundant class of marine dissolved organic matter (DOM), which must be hydrolyzed by extracellular enzymes prior to uptake by heterotrophic microbes. Pelagic microbial communities differ in their ability to access polysaccharides: some communities are completely incapable of accessing certain polysaccharides which are readily hydrolyzed elsewhere. I measured enzymatic hydrolysis of structurally defined polysaccharides in the Gulf of Mexico and in Svalbard fjords (Arctic Ocean), and investigated the factors that influenced enzyme activities. Arctic communities were able to access a narrower range of polysaccharide structures than Gulf of Mexico surface water communities, but Gulf of Mexico mesopelagic (>100 m depth) communities also accessed a limited range of polysaccharides. Attempts to induce expression of pullulanase, which was not present in Arctic samples, suggested that the Arctic communities were totally incapable of expressing pullulanase, most likely for lack of the necessary genes. Half-lives of extracellular enzymes in seawater were on the order of tens to hundreds of hours, long enough for extracellular enzymes to become decoupled from the microbes that produced them. These results point to functional differences in DOM processing among marine microbial communities, indicating that DOM lability is a function of the microbial community present as well as DOM chemical characteristics

Evidence for the Priming Effect in a Planktonic Estuarine Microbial Community

The “priming effect,” in which addition of labile substances changes the remineralization rate of recalcitrant organic matter, has been intensively studied in soils, but is less well-documented in aquatic systems. We investigated the extent to which additions of nutrients or labile organic carbon could influence remineralization rates of 14C-labeled, microbially-degraded, phytoplankton-derived organic matter (OM) in microcosms inoculated with microbial communities drawn from Grove Creek Estuary in coastal Georgia, USA. We found that amendment with labile protein plus phosphorus increased remineralization rates of degraded, phytoplankton-derived OM by up to 100%, whereas acetate slightly decreased remineralization rates relative to an unamended control. Addition of ammonium and phosphate induced a smaller effect, whereas addition of ammonium alone had no effect. Counterintuitively, alkaline phosphatase activities increased in response to the addition of protein under P-replete conditions, indicating that production of enzymes unrelated to the labile priming compound may be a mechanism for the priming effect. The observed priming effect was transient: after 36 days of incubation roughly the same quantity of organic carbon had been mineralized in all treatments including no-addition controls. This timescale is on the order of the typical hydrologic residence times of well-flushed estuaries suggesting that priming in estuaries has the potential to influence whether OC is remineralized in situ or exported to the coastal ocean

Carbon in the Deep Biosphere: Forms, Fates, and Biogeochemical Cycling

Building on the synthesis of carbon reservoirs in Earth\u27s subsurface, this chapter focuses on the forms, cycling, and fate of the carbon supporting microbial life in the terrestrial and marine subsurface. As the subsurface is estimated to host a vast reservoir of life on Earth, identifying the carbon compounds that life uses for energy and growth is key to understanding ecosystem functioning in the past and at present, and also for extrapolating these findings to the search for life in the universe. This chapter highlights advances in quantifying small carbon compounds, measuring rates of carbon turnover, and the fate of carbon in the deep biosphere

Carbon in the Deep Biosphere: Forms, Fates, and Biogeochemical Cycling

Building on the synthesis of carbon reservoirs in Earth\u27s subsurface, this chapter focuses on the forms, cycling, and fate of the carbon supporting microbial life in the terrestrial and marine subsurface. As the subsurface is estimated to host a vast reservoir of life on Earth, identifying the carbon compounds that life uses for energy and growth is key to understanding ecosystem functioning in the past and at present, and also for extrapolating these findings to the search for life in the universe. This chapter highlights advances in quantifying small carbon compounds, measuring rates of carbon turnover, and the fate of carbon in the deep biosphere

Picky, hungry eaters in the cold: persistent substrate selectivity among polar pelagic microbial communities

Polar pelagic microbial communities access a narrower range of polysaccharide substrates than communities at lower latitudes. For example, the glucose-containing polysaccharide pullulan is typically not hydrolyzed in fjord waters of Svalbard, even though pullulan is rapidly hydrolyzed in sediments from Svalbard fjords, other polysaccharides are hydrolyzed rapidly in Svalbard waters, and pullulan is hydrolyzed rapidly in temperate waters. The purpose of this study was to investigate potential factors preventing hydrolysis of pullulan in Svalbard fjord waters. To this end, in two separate years, water from Isfjorden, Svalbard, was amended with different carbon sources and/or additional nutrients in order to determine whether increasing the concentration of these potentially-limiting factors would lead to measurable enzymatic activity. Addition of nitrate, phosphate, glucose, or amino acids did not yield detectable pullulan hydrolysis. The only treatment that led to detectable pullulan hydrolysis was extended incubation after the addition of maltotriose (a subunit of pullulan, and potential inducer of pullulanase). In these fjords, the ability to enzymatically access pullulan is likely confined to numerically minor members of the pelagic microbial community. These results are consistent with the hypothesis that pelagic microbial communities at high latitudes exhibit streamlined functionality, focused on a narrower range of substrates, than their temperate counterparts

Patterns of extracellular enzyme activities and microbial metabolism in an Arctic fjord of Svalbard and in the northern Gulf of Mexico: contrasts in carbon processing by pelagic microbial communities

The microbial community composition of polar and temperate ocean waters differs substantially, but the potential functional consequences of these differences are largely unexplored. We measured bacterial production, glucose metabolism, and the abilities of microbial communities to hydrolyze a range of polysaccharides in an Arctic fjord of Svalbard (Smeerenburg Fjord), and thus to initiate remineralization of high-molecular weight organic matter. We compared these data with similar measurements previously carried out in the northern Gulf of Mexico in order to investigate whether differences in the spectrum of enzyme activities measurable in Arctic and temperate environments are reflected in “downstream” aspects of microbial metabolism (metabolism of monomers and biomass production). Only four of six polysaccharide substrates were hydrolyzed in Smeerenburg Fjord; all were hydrolyzed in the upper water column of the Gulf. These patterns are consistent on an interannual basis. Bacterial protein production was comparable at both locations, but the pathways of glucose utilization differed. Glucose incorporation rate constants were comparatively higher in Svalbard, but glucose respiration rate constants were higher in surface waters of the Gulf. As a result, at the time of sampling ca. 75% of the glucose was incorporated into biomass in Svalbard, but in the northern Gulf of Mexico most of the glucose was respired to CO2. A limited range of enzyme activities is therefore not a sign of a dormant community or one unable to further process substrates resulting from extracellular enzymatic hydrolysis. The ultimate fate of carbohydrates in marine waters, however, is strongly dependent upon the specific capabilities of heterotrophic microbial communities in these disparate environments

Drill site locations from MPSV GREATSHIP MANISHA IODP-347 cruise in the Baltic Sea in 2013 (IODP-347 Microbial Quantification project)

Dataset: IODP-347 drill site locationsIn 2013, Integrated Ocean Drilling Program Expedition 347 sampled six subbasins within the Baltic Sea Basin in an effort to understand the sedimentological record of climate dynamics over the last 140,000 years. These sites, including Bornholm Basin (BSB-7), Lille Belt (BSB-3), and Anholt Loch (BSB-9), were selected because they contain varved, rapidly deposited sediments that represent an archive of paleoclimatological information spanning from the last glacial cycle. This expedition was led by Dr. Bo Barker Jørgensen of Aarhus University and Dr. Thomas Andrén of Södertörn University aboard the vessel MPSV GREATSHIP MANISHA. Data included here are dates sampled, latitude and longitude, and depth of overlying water. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/641342NSF Division of Ocean Sciences (NSF OCE) OCE-143159