| name | element-cycling |
| description | Route biogeochemical / elemental cycling annotation for shotgun metagenomics and MAGs: carbon (C), nitrogen (N), sulfur (S), iron (Fe), phosphorus (P), hydrogen (H2/H), oxygen (O), methane (CH4), and other metals/metalloids (Mn, As, Se, …) via METABOLIC, MEBS, FeGenie, plus DRAM/KEGG/eggNOG backups. Use when asking which elemental transformations a community or MAG can perform — not for taxonomy tables. Child skills: metabolic, mebs, fegenie. Related: dram, kegg, eggnog-mapper, gapseq. Route via microbial-mining.
|
| license | MIT |
| category | orchestration |
| tags | ["element-cycling","biogeochemistry","C","N","S","Fe","P","CH4","METABOLIC","MEBS","FeGenie"] |
| stage | mining |
Element cycling (biogeochemistry)
Elemental / biogeochemical capacity is a mining track after gene call on
assemblies or QC-filtered MAGs. Hits are genetic potential — not fluxes.
Elements to report (pin which you claim)
| Element / cycle | Typical transformations | Prefer |
|---|
| C (carbon) | Fixation, fermentation, respiration, C1 | metabolic · dram · kegg |
| N (nitrogen) | N₂ fixation, nitrification, denitrification, anammox, DNRA, ammonification | metabolic · mebs · dram |
| S (sulfur) | Sulfate/sulfite reduction, oxidation, disproportionation, organic S | mebs · metabolic · dram |
| Fe (iron) | Acquisition, siderophores, Fe²⁺/Fe³⁺ redox, storage, magnetosome | fegenie · mebs · metabolic |
| P (phosphorus) | Uptake, solubilization, poly-P, organic P | metabolic · dram · kegg |
| H / H₂ | Hydrogenases, H₂ metabolism | metabolic · dram |
| O | Aerobic respiration markers / O-related scores | mebs · metabolic |
| CH₄ (methane) | Methanogenesis, methanotrophy | mebs · metabolic · dram |
| Other metals | Mn, As, Se, Hg, … (tool “other” / KO modules) | metabolic · kegg · eggnog-mapper |
Analytical thinking
| Claim | Prefer | Do not treat as |
|---|
| Multi-element MAG/community diagrams (C/N/S/…) | metabolic (METABOLIC-G/C) | Measured rates |
| Entropy scores for S (and N/O/CH₄/Fe) machinery | mebs | Pathway proof without genes |
| Iron acquisition / redox / siderophores / magnetosome | fegenie | Sole Fe claim from generic KO only |
| Distilled metabolism tables (broad) | dram | Element-specific FeGenie depth |
| KO/module maps (licensed KEGG) | kegg / eggnog-mapper | Bulk redistributable KEGG dump |
| GEMs / flux hypotheses | gapseq (± alphagem) | Element HMM presence alone |
Hard rules:
- Name which elements and which tool/DB version produced each claim
- Do not merge METABOLIC diagrams, MEBS scores, FeGenie tables, and HUMAnN
pathways unlabeled
- Low-completeness MAGs under-call pathways — filter with
mag-qc first
- Siderophores / secondary metabolites ≠ proven secretion (
fegenie / antismash)
Decision tree
Element / biogeochem need?
│
├─ Broad C / N / S (+ other) on MAGs ± reads → metabolic
├─ Sulfur-focused scores (± N, O, CH₄, Fe) → mebs
├─ Iron genes / neighborhoods / siderophores → fegenie
├─ Distilled multi-DB metabolism sheets → dram
├─ KO / modules → kegg / eggnog-mapper
├─ CAZymes (organic C polymer) → dbcan
├─ GEMs → gapseq
└─ Unsure → this hub + microbial-mining
Related skills
metabolic · mebs · fegenie · dram · dbcan · kegg ·
eggnog-mapper · gapseq · alphagem · antismash · microbial-mining ·
tool-selection
