Evidence of nitrification associated with globally distributed pelagic jellyfish

Often considered detrimental to the environment and human activities, jellyfish blooms are increasing in several coastal regions worldwide. Yet, the overall effect of these outbreaks on ecosystem productivity and structure are not fully understood. Here we provide evidence for a so far unanticipated role of jellyfish in marine nitrogen cycling. Pelagic jellyfish release nitrogen as a metabolic waste product in form of ammonium. Yet, we observed high rates of nitrification (NH4+ → NO3−, 5.7–40.8 nM gWW−1 [wet weight] h−1) associated with the scyphomedusae Aurelia aurita, Chrysaora hysoscella, and Chrysaora pacifica and low rates of incomplete nitrification (NH4+ → NO2−, 1.0–2.8 nM gWW−1 h−1) associated with Chrysaora fulgida, C. hysoscella, and C. pacifica. These observations indicate that microbes living in association with these jellyfish thrive by oxidizing the readily available ammonia to nitrite and nitrate. The four studied species have a large geographic distribution and exhibit frequent population outbreaks. We show that, during such outbreaks, jellyfish‐associated release of nitrogen can provide more than 100% of the nitrogen required for primary production. These findings reveal a so far overlooked pathway when assessing pelagic nitrification rates that might be of particular relevance in nitrogen depleted surface waters and at high jellyfish population densities

Microbes with higher metabolic independence are enriched in human gut microbiomes under stress

A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health versus IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments

Evidence of nitrification associated with globally distributed pelagic jellyfish

Bioavailable nitrogen is a scarce resource in most of the surface oceanand often limits primary productivity. Although Pelagic jellyfish excretesubstantial amounts of ammonia (the preferred form of nitrogen formost phytoplankton), they are overlooked players in marine nitrogencycling. Here, we observed high rates of nitrification (NH4+ → NO3-, 5.7– 40.8 nM gWW-1 (wet weight) h-1) associated with the scyphomedusaeAurelia aurita, Chrysaora hysoscella and Chrysaora pacifica and low ratesof incomplete nitrification (NH4+ → NO2-, 1-2.7 nM gWW-1 h-1)associated with Chrysaora fulgida, Chrysaora hysoscella and Chrysaorapacifica. These observations indicate that microbes living in associationwith the jellyfish thrive by oxidizing the readily available ammonia tonitrite and nitrate. The four studied species are abundant over a largegeographic distribution and exhibit frequent population outbreaks. Weshow that, during such outbreaks, jellyfish-associated release of nitrogencan provide more than 100% of the nitrogen required for primaryproduction. These findings reveal a so far overlooked pathway whenassessing pelagic nitrification rates that might be of particular relevancein nitrogen depleted surface waters and at high jellyfish populationdensities

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus

Nitrite-oxidizing bacteria (NOB) have conventionally been regarded as a highly specialized functional group responsible for the production of nitrate in the environment. However, recent culture-based studies suggest that they have the capacity to lead alternative lifestyles, but direct environmental evidence for the contribution of marine nitrite oxidizers to other processes has been lacking to date. We report on the alternative biogeochemical functions, worldwide distribution, and sometimes high abundance of the marine NOB Nitrococcus. These largely overlooked bacteria are capable of not only oxidizing nitrite but also reducing nitrate and producing nitrous oxide, an ozone-depleting agent and greenhouse gas. Furthermore, Nitrococcus can aerobically oxidize sulfide, thereby also engaging in the sulfur cycle. In the currently fast-changing global oceans, these findings highlight the potential functional switches these ubiquitous bacteria can perform in various biogeochemical cycles, each with distinct or even contrasting consequences

Metabolic independence drives gut microbial colonization and resilience in health and disease

Background: Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. Results: Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. Conclusions: These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of “dysbiosis” that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.</p

Additional file 10 of Metabolic independence drives gut microbial colonization and resilience in health and disease

Additional file 10. a List of genomes from healthy individuals and individuals with IBD. b Module completion values across genomes

Additional file 9 of Metabolic independence drives gut microbial colonization and resilience in health and disease

Additional file 9. Description of HMI vs. LMI populations. a Taxonomic assignments and genome size estimates for high- and low-metabolic independence populations. b KEGG module completeness information for high- and low-metabolic independence populations. c Raw KEGG module enrichment information for high- and low-metabolic independence populations. d KEGG module enrichment and categorical information for the 33 modules enriched in high-metabolic independence populations. e and f Completeness information for the 33 modules enriched in high-metabolic independence populations in all high- and low-metabolic independence populations

Additional file 1 of Metabolic independence drives gut microbial colonization and resilience in health and disease

Additional file 1. Description of FMT study and stool samples collected. a Description of FMT donor stool samples and SRA accession numbers. b Description of FMT recipient samples and SRA accession numbers. c Description of transplantation events

Additional file 4 of Metabolic independence drives gut microbial colonization and resilience in health and disease

Additional file 4. Description of MAGs. a Summary statistics and taxonomic assignments for MAGs. b and c Detection of Donor A and Donor B MAGs in FMT metagenomes, respectively. d and e Detection of Donor A and Donor B MAGs in global gut metagenomes, respectively. f and g Detection summary statistics of Donor A and Donor B MAGs in global gut metagenomes, respectively. h and i Mean non-outlier coverage of Donor A and Donor B MAG single-copy core genes in FMT metagenomes

Additional file 3 of Metabolic independence drives gut microbial colonization and resilience in health and disease

Additional file 3. Description of FMT metagenomes and co-assemblies. a Metagenome SRA accession numbers and number of metagenomic short-reads sequenced and mapped to co-assemblies and MAGs. b) Phylum level taxonomic composition of metagenomes. c) Genus level taxonomic composition of metagenomes. d) Summary statistics for contigs from metagenome co-assemblies