Assimilatory nitrate utilization by bacteria on the West Florida Shelf as determined by stable isotope probing and functional microarray analysis

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate

Photosynthetic microalgae are responsible for 50% of the global atmospheric CO₂ fixation into organic matter and hold potential as a renewable bioenergy source. Their metabolic interactions with the surrounding microbial community (the algal microbiome) play critical roles in carbon cycling, but due to methodological limitations, it has been challenging to examine how community development is influenced by spatial proximity to their algal host. Here we introduce a copolymer-based porous microplate to co-culture algae and bacteria, where metabolites are constantly exchanged between the microorganisms while maintaining physical separation. In the microplate, we found that the diatom Phaeodactylum tricornutum accumulated to cell abundances ~20 fold higher than under normal batch conditions due to constant replenishment of nutrients through the porous structure. We also demonstrate that algal-associated bacteria, both single isolates and complex communities, responded to inorganic nutrients away from their host as well as organic nutrients originating from the algae in a spatially predictable manner. These experimental findings coupled with a mathematical model suggest that host proximity and algal culture growth phase impact bacterial community development in a taxon-specific manner through organic and inorganic nutrient availability. Our novel system presents a useful tool to investigate universal metabolic interactions between microbes in aquatic ecosystems.

Metabolic Functional Community Diversity of Associated Bacteria during the Degradation of Phytoplankton from a Drinking Water Reservoir

In the drinking water reservoir ecosystem, phytoplankton and bacteria play important roles in shaping freshwater health and function. In this work, the associated bacterial community functional diversity during degradation of phytoplankton was determined using the substrate utilization profiling (BIOLOG) technique, meanwhile, the composition and concentration of phytoplankton were examined using a microscope. The results indicated that Euglena decreased 58.33% from 0 to 38 d, while the smallest degradation of Bacillariophyta was 20.19%. Average well color development (AWCD_590nm) increased during the static periods from 0 to 38 d; however, the AWCD_590nm of 18 and 38 d had no significant difference (p < 0.05). The Simpson’s index (D) was in accordance with Shannon’s diversity (H) and species richness(S); it was measured to be18 > 38 > 5 > 0 d. There were significant differences in the pattern and level of carbon sources used by the phytoplankton-associated bacteria. In addition, the principle component analyses (PCA) suggested that the first principle component (PC1) and the second principle component (PC2) explained 46.76% and 21.49% of the total variation for bacterial community, respectively. Redundancy analysis (RDA) revealed that cell abundance of phytoplankton was negatively correlated with the AWCD_590nm, amino acids and other functional indexes. Therefore, the data suggest that there are differences in the phytoplankton-associated bacterial community functional diversity during different static stages of water samples collected from the drinking water reservoir.

Artificial substrata increase pond farming density of grass carp (Ctenopharyngodon idella) by increasing the bacteria that participate in nitrogen and phosphorus cycles in pond water

Aquaculture has become a primary method to produce various aquatic products, and intensive aquaculture technologies have become commercially important. To improve the efficiency of intensive aquaculture per unit area without reducing the growth rate of cultured fish, the present study explored the potential of artificial substrata in ponds. Our results showed that the concentrations of total nitrogen (TN) and total phosphorous (TP) in the ponds with different stocking densities of grass carp were lower than those in the control group in most cases. Further, the feed conversion rate of grass carp was significantly reduced by introducing these artificial substrata, and the culture density could be significantly increased without reducing the growth rates of these fish. Artificial substrata also significantly enriched specific bacteria and changed the structure of the microbiota in pond water. The relative abundance of Proteobacteria was significantly increased, and bacteria closely related to N and P cycles, such as Hyphomicrobium, Chitinimonas, Legionella, Shewanella, Roseiflexus, and Planktothrix were significantly enhanced. These results showed that the artificial substratum could increase TN and TP removal in aquaculture pond water by enriching N and P cycle-related bacteria, thus significantly increasing the specific growth rate of grass carp and significantly reducing their feed conversion rate. Finally, the stocking density of grass carp and the yield per unit area of pond could be increased without reducing the growth rate.

Characterization of bacterioplankton communities from a hatchery recirculating aquaculture system (RAS) for juvenile sole (Solea senegalensis) production

There is a growing consensus that future technological developments of aquaculture systems should account for the structure and function of microbial communities in the whole system and not only in fish guts. In this study, we aimed to investigate the composition of bacterioplankton communities of a hatchery recirculating aquaculture system (RAS) used for the production of Senegalese sole (Solea senegalensis) juveniles. To this end, we used a 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses to characterize the bacterioplankton communities of the RAS and its water supply. Overall, the most abundant orders were Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales, Flavobacteriales, Lactobacillales, Thiotrichales, Burkholderiales and Bdellovibrionales. Although we found a clear distinction between the RAS and the water supply bacterioplankton communities, most of the abundant OTUs (≥50 sequences) in the hatchery RAS were also present in the water supply. These included OTUs related to Pseudoalteromonas genus and the Roseobacter clade, which are known to comprise bacterial members with activity against Vibrio fish pathogens. Overall, in contrast to previous findings for sole grow-out RAS, our results suggest that the water supply may influence the bacterioplankton community structure of sole hatchery RAS. Further studies are needed to investigate the effect of aquaculture practices on RAS bacterioplankton communities and identification of the key drivers of their structure and diversity.

Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community

To quantitatively link microbial identity with biogeochemical function, we carried out 14 simultaneous stable isotope probing experiments with organic and inorganic C and N substrates to measure the isotope incorporation by over one hundred co-occurring eukaryotic and prokaryotic populations in a coastal community. We found that nitrate was the most commonly incorporated substrate, and that light-driven carbon fixation was carried out by some bacterial taxa from the Flavobacteriales and OM60 (NOR5) clade, in addition to photoautotrophic phytoplankton. We found that organisms that incorporated starch, maltose, glucose, lactose and bicarbonate were phylogenetically clustered, suggesting that specific bacterial lineages specialized in the incorporation of these substrates. The data further revealed that coastal microorganisms spanned a range of resource utilization strategies from generalists to specialists and demonstrated a high level of substrate partitioning, with two thirds of taxa exhibiting unique substrate incorporation patterns and the remaining third shared by no more than three OTUs each. Specialists exhibited more extreme incorporation levels (high or low), whereas generalists displayed more intermediate activity levels. These results shed valuable insights into the bottom-up ecological strategies enabling the persistence of high microbial diversity in aquatic ecosystems.

The roles of cyanobacterial bloom in nitrogen removal

Annually occurred cyanobacterial bloom aggravated eutrophication situation and changed the lacustrine ecosystem components. Recently, high concentration of bloom cyanobacteria had been found to accelerate total nitrogen (TN) removal. However, the contribution of cyanobacterial bloom to TN removal remained unclear. In this study, microcosms with different density of bloom cyanobacteria were constructed and quantitative PCR and structural equation modelling (SEM) were used to analyze the microbes, environmental variables and the causal relationship to TN removal. Total bacteria, ammonia-oxidizing archaea and nirS gene abundances were indirectly influenced by cyanobacteria biomass and all of them had a direct effect on TN removal. SEM confirmed that cyanobacteria made a direct contribution to ammonium‑nitrogen (NH₄⁺-N) level in water and induced nitrification activity, which favored the process of denitrification by supplying substrate and aggravating the anoxic status. These results strongly suggested that an increased cyanobacteria biomass had strong impacts on mineralization, nitrification and denitrification by mediating TN, dissolved organic carbon and dissolved oxygen directly and subsequently influenced the nitrifiers and denitrifiers.

Different Bacterial Communities Involved in Peptide Decomposition between Normoxic and Hypoxic Coastal Waters

Proteins and peptides are key components of the labile dissolved organic matter pool in marine environments. Knowing which types of bacteria metabolize peptides can inform the factors that govern peptide decomposition and further carbon and nitrogen remineralization in marine environments. A ¹³C-labeled tetrapeptide, alanine-valine-phenylalanine-alanine (AVFA), was added to both surface (normoxic) and bottom (hypoxic) seawater from a coastal station in the northern Gulf of Mexico for a 2-day incubation experiment, and bacteria that incorporated the peptide were identified using DNA stable isotope probing (SIP). The decomposition rate of AVFA in the bottom hypoxic seawater (0.018–0.035 μM h^-1) was twice as fast as that in the surface normoxic seawater (0.011–0.017 μM h^-1). SIP experiments indicated that incorporation of ¹³C was highest among the Flavobacteria, Sphingobacteria, Alphaproteobacteria, Acidimicrobiia, Verrucomicrobiae, Cyanobacteria, and Actinobacteria in surface waters. In contrast, highest ¹³C-enrichment was mainly observed in several Alphaproteobacteria (Thalassococcus, Rhodobacteraceae, Ruegeria) and Gammaproteobacteria genera (Colwellia, Balneatrix, Thalassomonas) in the bottom water. These data suggest that a more diverse group of both oligotrophic and copiotrophic bacteria may be involved in metabolizing labile organic matter such as peptides in normoxic coastal waters, and several copiotrophic genera belonging to Alphaproteobacteria and Gammaproteobacteria and known to be widely distributed may contribute to faster peptide decomposition in the hypoxic waters.

Intraclade Heterogeneity in Nitrogen Utilization by Marine Prokaryotes Revealed Using Stable Isotope Probing Coupled with Tag Sequencing (Tag-SIP)

Nitrogen can greatly influence the structure and productivity of microbial communities through its relative availability and form. However, the roles of specific organisms in the uptake of different nitrogen species remain poorly characterized. Most studies seeking to identify agents of assimilation have been correlative, indirectly linking activity measurements (e.g., nitrate uptake) with the presence or absence of biological markers, particularly functional genes and their transcripts. Evidence is accumulating of previously underappreciated functional diversity in major microbial subpopulations, which may confer physiological advantages under certain environmental conditions leading to ecotype divergence. This microdiversity further complicates our view of genetic variation in environmental samples requiring the development of more targeted approaches. Here, next-generation tag sequencing was successfully coupled with stable isotope probing (Tag-SIP) to assess the ability of individual phylotypes to assimilate a specific N source. Our results provide the first direct evidence of nitrate utilization by organisms thought to lack the genes required for this process including the heterotrophic clades SAR11 and the Archaeal Marine Group II. Alternatively, this may suggest the existence of tightly coupled metabolisms with primary assimilators, e.g., symbiosis, or the rapid and efficient scavenging of recently released products by highly active individuals. These results may be connected with global dominance often seen with these clades, likely conferring an advantage over other clades unable to access these resources. We also provide new direct evidence of in situ nitrate utilization by the cyanobacterium Prochlorococcus in support of recent findings. Furthermore, these results revealed widespread functional heterogeneity, i.e., different levels of nitrogen assimilation within clades, likely reflecting niche partitioning by ecotypes.

Methanogenic paraffin degradation proceeds via alkane addition to fumarate by 'Smithella' spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens

Anaerobic microbial biodegradation of recalcitrant, water-insoluble substrates, such as paraffins, presents unique metabolic challenges. To elucidate this process, a methanogenic consortium capable of mineralizing long-chain n-paraffins (C28 -C50 ) was enriched from San Diego Bay sediment. Analysis of 16S rRNA genes indicated the dominance of Syntrophobacterales (43%) and Methanomicrobiales (26%). Metagenomic sequencing allowed draft genome assembly of dominant uncultivated community members belonging to the bacterial genus Smithella and the archaeal genera Methanoculleus and Methanosaeta. Five contigs encoding homologs of the catalytic subunit of alkylsuccinate synthase (assA) were detected. Additionally, mRNA transcripts for these genes, including a homolog binned within the 'Smithella' sp. SDB genome scaffold, were detected via RT-PCR, implying that paraffins are activated via 'fumarate addition'. Metabolic reconstruction and comparison with genome scaffolds of uncultivated n-alkane degrading 'Smithella' spp. are consistent with the hypothesis that syntrophically growing 'Smithella' spp. may achieve reverse electron transfer by coupling the reoxidation of ETFred to a membrane-bound FeS oxidoreductase functioning as an ETF:menaquinone oxidoreductase. Subsequent electron transfer could proceed via a periplasmic formate dehydrogenase and/or hydrogenase, allowing energetic coupling to hydrogenotrophic methanogens such as Methanoculleus. Ultimately, these data provide fundamental insight into the energy conservation mechanisms that dictate interspecies interactions salient to methanogenic alkane mineralization.

Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms

Diatoms are a dominant group of eukaryotic phytoplankton that contribute substantially to global primary production and the cycling of important elements such as carbon and nitrogen. Heterotrophic bacteria, including members of the gammaproteobacteria, are commonly associated with diatom populations and may rely on them for organic carbon while potentially competing with them for other essential nutrients. Considering that bacterioplankton drive oceanic release of CO 2 (i.e., bacterial respiration) while diatoms drive ocean carbon sequestration vial the biological pump, the outcome of such competition could influence the direction and magnitude of carbon flux in the upper ocean. Nitrate availability is commonly a determining factor for the growth of diatom populations, particularly in coastal and upwelling regions. Diatoms as well as many bacterial species can utilize nitrate, however the ability of bacteria to compete for nitrate may be hindered by carbon limitation. Here we have developed a genetically tractable model system using the pennate diatom Phaeodactylum tricornutum and the widespread heterotrophic bacteria Alteromonas macleodii to examine carbon-nitrogen dynamics. While subsisting solely on P. tricornutum derived carbon, A. macleodii does not appear to be an effective competitor for nitrate, and may in fact benefit the diatom; particularly in stationary phase. However, allochthonous dissolved organic carbon addition in the form of pyruvate triggers A. macleodii proliferation and nitrate uptake, leading to reduced P. tricornutum growth. Nitrate reductase deficient mutants of A. macleodii (ΔnasA) do not exhibit such explosive growth and associated competitive ability in response to allochthonous carbon when nitrate is the sole nitrogen source, but could survive by utilizing solely P. tricornutum-derived nitrogen. Furthermore, allocthonous carbon addition enables wild-type A. macleodii to rescue nitrate reductase deficient P. tricornutum populations from nitrogen starvation, and RNA-seq transcriptomic evidence supports nitrogen-based interactions between diatoms and bacteria at the molecular level. This study provides key insights into the roles of carbon and nitrogen in phytoplankton-bacteria dynamics and lays the foundation for developing a mechanistic understanding of these interactions using co-culturing and genetic manipulation.

Effects of electron acceptors on soluble reactive phosphorus in the overlying water during algal decomposition

Endogenous phosphorus (P) release from sediments is an important factor to cause eutrophication and, hence, algal bloom in lakes in China. Algal decomposition depletes dissolved oxygen (DO) and causes anaerobic conditions and therefore increases P release from sediments. As sediment P release is dependent on the iron (Fe) cycle, electron acceptors (e.g., NO3 (-), SO4 (2-), and Mn(4+)) can be utilized to suppress the reduction of Fe(3+) under anaerobic conditions and, as such, have the potential to impair the release of sediment P. Here, we used a laboratory experiment to test the effects of FeCl3, MnO2, and KNO3 on soluble reactive phosphorus (SRP) concentration and related chemical variables in the overlying water column during algal decomposition at different algal densities. Results showed that algal decomposition significantly depleted DO and thereby increased sediment Fe-bound P release. Compared with the control, addition of FeCl3 significantly decreased water SRP concentration through inhibiting sediment P release. Compared with FeCl3, addition of MnO2 has less potential to suppress sediment P release during algal decomposition. Algal decomposition has the potential for NO3 (-) removal from aquatic ecosystem through denitrification and by that alleviates the suppressing role of NO3 (-) on sediment P release. Our results indicated that FeCl3 and MnO2 could be efficient in reducing sediment P release during algal decomposition, with the strongest effect found for FeCl3; large amounts of NO3 (-) were removed from the aquatic ecosystem through denitrification during algal decomposition. Moreover, the amounts of NO3 (-) removal increased with increasing algal density.

Ubiquity and diversity of heterotrophic bacterial nasA genes in diverse marine environments

Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB). In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase) gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides) bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III). Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating that NAB may be active participants contributing to the bloom dynamics. Our statistical results suggested that salinity, temperature and nitrate may be some of the key environmental factors controlling the composition and dynamics of the marine NAB communities.

Urea uptake and carbon fixation by marine pelagic bacteria and archaea during the Arctic summer and winter seasons

How Arctic climate change might translate into alterations of biogeochemical cycles of carbon (C) and nitrogen (N) with respect to inorganic and organic N utilization is not well understood. This study combined 15N uptake rate measurements for ammonium, nitrate, and urea with 15N- and 13C-based DNA stable-isotope probing (SIP). The objective was to identify active bacterial and archeal plankton and their role in N and C uptake during the Arctic summer and winter seasons. We hypothesized that bacteria and archaea would successfully compete for nitrate and urea during the Arctic winter but not during the summer, when phytoplankton dominate the uptake of these nitrogen sources. Samples were collected at a coastal station near Barrow, AK, during August and January. During both seasons, ammonium uptake rates were greater than those for nitrate or urea, and nitrate uptake rates remained lower than those for ammonium or urea. SIP experiments indicated a strong seasonal shift of bacterial and archaeal N utilization from ammonium during the summer to urea during the winter but did not support a similar seasonal pattern of nitrate utilization. Analysis of 16S rRNA gene sequences obtained from each SIP fraction implicated marine group I Crenarchaeota (MGIC) as well as Betaproteobacteria, Firmicutes, SAR11, and SAR324 in N uptake from urea during the winter. Similarly, 13C SIP data suggested dark carbon fixation for MGIC, as well as for several proteobacterial lineages and the Firmicutes. These data are consistent with urea-fueled nitrification by polar archaea and bacteria, which may be advantageous under dark conditions.

A microarray for assessing transcription from pelagic marine microbial taxa

Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.

Molecular analysis of bacterial communities and detection of potential pathogens in a recirculating aquaculture system for Scophthalmus maximus and Solea senegalensis

The present study combined a DGGE and barcoded 16S rRNA pyrosequencing approach to assess bacterial composition in the water of a recirculating aquaculture system (RAS) with a shallow raceway system (SRS) for turbot (Scophthalmus maximus) and sole (Solea senegalensis). Barcoded pyrosequencing results were also used to determine the potential pathogen load in the RAS studied. Samples were collected from the water supply pipeline (Sup), fish production tanks (Pro), sedimentation filter (Sed), biofilter tank (Bio), and protein skimmer (Ozo; also used as an ozone reaction chamber) of twin RAS operating in parallel (one for each fish species). Our results revealed pronounced differences in bacterial community composition between turbot and sole RAS, suggesting that in the systems studied there is a strong species-specific effect on water bacterial communities. Proteobacteria was the most abundant phylum in the water supply and all RAS compartments. Other important taxonomic groups included the phylum Bacteriodetes. The saltwater supplied displayed a markedly lower richness and appeared to have very little influence on bacterial composition. The following potentially pathogenic species were detected: Photobacterium damselae in turbot (all compartments), Tenacibaculum discolor in turbot and sole (all compartments), Tenacibaculum soleae in turbot (all compartments) and sole (Pro, Sed and Bio), and Serratia marcescens in turbot (Sup, Sed, Bio and Ozo) and sole (only Sed) RAS. Despite the presence of these pathogens, no symptomatic fish were observed. Although we were able to identify potential pathogens, this approach should be employed with caution when monitoring aquaculture systems, as the required phylogenetic resolution for reliable identification of pathogens may not always be possible to achieve when employing 16S rRNA gene fragments.

Use of functional gene arrays for elucidating in situ biodegradation

Microarrays have revolutionized the study of microbiology by providing a high-throughput method for examining thousands of genes with a single test and overcome the limitations of many culture-independent approaches. Functional gene arrays (FGA) probe a wide range of genes involved in a variety of functions of interest to microbial ecology (e.g., carbon degradation, N fixation, metal resistance) from many different microorganisms, cultured and uncultured. The most comprehensive FGA to date is the GeoChip array, which targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulfur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB). Since the development of GeoChips, many studies have been performed using this FGA and have shown it to be a powerful tool for rapid, sensitive, and specific examination of microbial communities in a high-throughput manner. As such, the GeoChip is well-suited for linking geochemical processes with microbial community function and structure. This technology has been used successfully to examine microbial communities before, during, and after in situ bioremediation at a variety of contaminated sites. These studies have expanded our understanding of biodegradation and bioremediation processes and the associated microorganisms and environmental conditions responsible. This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation.

Taxon-specific C/N relative use efficiency for amino acids in an estuarine community

Microbial activity plays a critical role in determining the nutrient status of an ecosystem (i.e. N or C limitation). While the balance of C/N assimilation has been measured at the whole community scale, quantitative detection of N and C assimilation from a single substrate at the scale of individual taxa has not been carried out. We recently developed Chip-SIP, a microarray and NanoSIMS-based method for linking microbial phylogeny and function that allows simultaneous measurement of (15)N and (13)C incorporation. Here, we measured the relative incorporation of C and N from dual-labeled substrates by individual microbial taxa in bottle incubations of samples collected from an estuary. Incubation times < 24 h were sufficient to successfully detect active microbes incorporating (15)N ammonium. In subsequent experiments, we used the incorporation of labeled amino acids (AAs) as a proxy for heterotrophic activity and showed different levels of incorporation among different taxonomic groups. Taxon-specific differences in the net incorporation of AA-derived C and N indicate that the C/N relative use efficiency ranged from 0.8 to 1.4, where 1 reflects stoichiometric incorporation of C and N. Our results revealed that microbial organic matter processing is affected by taxon-specific physiological diversity, both in terms of general activity levels and in the ratio of assimilated C/N.