07 Hotspot Interactions
Jupyter notebook from the SSO Subsurface Community Ecology — Spatial Structure, Functional Gradients, and Hydrogeological Drivers project.
NB07: Community Hotspot Profiles and Inferred Metabolic Interactions¶
Goal: For each SSO well, profile the dominant community members and infer potential metabolic interactions — syntrophy, cross-feeding, electron donor-acceptor coupling, and competition. Build a conceptual interaction model for each biogeochemical hotspot identified in NB04/NB06.
Approach:
- Profile top 15 genera per well with their known metabolisms
- Identify co-occurring functional guilds (denitrifiers + iron reducers, syntrophs + methanogens, etc.)
- Map interactions onto the plume model: which wells host cooperative vs competitive metabolic networks?
- Compute guild co-occurrence across wells to identify spatially linked functional assemblages
In [1]:
import pandas as pd
import numpy as np
from pathlib import Path
from scipy.stats import spearmanr
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
import seaborn as sns
import warnings
warnings.filterwarnings('ignore')
DATA = Path('../data')
FIG = Path('../figures')
GRID = {
'SSO-U1': (2, 0), 'SSO-U2': (2, 1), 'SSO-U3': (2, 2),
'SSO-M4': (1, 0), 'SSO-M5': (1, 1), 'SSO-M6': (1, 2),
'SSO-L7': (0, 0), 'SSO-L8': (0, 1), 'SSO-L9': (0, 2),
}
WELL_ORDER = ['SSO-U1', 'SSO-U2', 'SSO-U3', 'SSO-M4', 'SSO-M5', 'SSO-M6',
'SSO-L7', 'SSO-L8', 'SSO-L9']
sed = pd.read_parquet(DATA / 'sso_sediment_asv.parquet')
total_per_well = sed.groupby('location')['abundance'].sum()
# Build genus relative abundance per well
genus_well = (sed.dropna(subset=['genus'])
.groupby(['location', 'genus'])['abundance'].sum()
.reset_index())
genus_well['rel_pct'] = genus_well.apply(
lambda r: r['abundance'] / total_per_well[r['location']] * 100, axis=1)
print("Data loaded")
Data loaded
1. Functional Guild Definitions¶
Assign each annotated genus to a metabolic guild. Guilds represent functional roles in the subsurface biogeochemical network — organisms within the same guild perform similar functions (potential competitors), while organisms in different guilds may be coupled through electron donor-acceptor relationships (potential syntrophs/cross-feeders).
In [2]:
# Assign genera to primary metabolic guilds
# Guild = the dominant metabolic mode that defines ecological role
GUILD_MAP = {
# Denitrifiers (NO3- -> N2) — consume plume nitrate
'denitrifier': ['Rhodanobacter', 'Castellaniella', 'Simplicispira', 'Zoogloea',
'Methyloversatilis', 'Hyphomicrobium', 'Sulfuritalea'],
# Nitrifiers (NH4+ -> NO2-/NO3-) — regenerate nitrate
'nitrifier': ['MND1', 'Candidatus Nitrosotalea', 'Nitrospira'],
# Iron reducers (Fe3+ -> Fe2+) — key metal cycling
'iron_reducer': ['Anaeromyxobacter', 'Geobacter', 'Rhodoferax'],
# Iron oxidizers (Fe2+ -> Fe3+) — plume-front process
'iron_oxidizer': ['Sideroxydans', 'Gallionella', 'Acidibacter'],
# Sulfate reducers (SO4 -> H2S)
'sulfate_reducer': ['Desulfobacca', 'Desulfovibrio', 'Desulfosporosinus'],
# Sulfur oxidizers (H2S/S0 -> SO4)
'sulfur_oxidizer': ['Arcobacter', 'Thiobacillus', 'Sulfuricurvum'],
# Syntrophs (obligate partners for methanogenesis/anaerobic degradation)
'syntroph': ['Syntrophus', 'Syntrophorhabdus', 'Pelotomaculum',
'Candidatus Cloacimonas'],
# Methane cyclers
'methanotroph': ['Candidatus Methanoperedens', 'Methylobacterium', 'Methylotenera'],
# Fermenters (complex C -> organic acids, H2, CO2)
'fermenter': ['Spirochaeta', 'Paenisporosarcina', 'Anoxybacillus',
'Trichococcus', 'Blautia'],
# Aerobic heterotrophs (O2 + organic C)
'aerobic_heterotroph': ['Pseudomonas', 'Sphingomonas', 'Massilia', 'Acinetobacter',
'Rhizomicrobium', 'Gordonia', 'Rhodococcus', 'Terrimonas',
'Candidatus Solibacter', 'Candidatus Omnitrophus',
'Comamonas', 'Duganella', 'Niastella', 'Gaiella', 'Afipia',
'Paenarthrobacter', 'Chujaibacter', 'Ferruginibacter'],
# Predators
'predator': ['Bdellovibrio'],
}
# Invert: genus -> guild
GENUS_GUILD = {}
for guild, genera in GUILD_MAP.items():
for g in genera:
GENUS_GUILD[g] = guild
# Known interaction types between guilds
GUILD_INTERACTIONS = {
('fermenter', 'syntroph'): 'cross-feeding: fermenters produce organic acids consumed by syntrophs',
('syntroph', 'sulfate_reducer'): 'syntrophic: syntrophs produce H2 consumed by sulfate reducers',
('syntroph', 'methanotroph'): 'syntrophic: H2/formate coupling in anaerobic methane oxidation',
('denitrifier', 'iron_reducer'): 'sequential: denitrifiers consume NO3-, creating conditions for Fe reduction',
('iron_oxidizer', 'iron_reducer'): 'iron cycle: oxidizers produce Fe3+, reducers regenerate Fe2+',
('sulfur_oxidizer', 'sulfate_reducer'): 'sulfur cycle: oxidizers produce SO4, reducers regenerate H2S',
('nitrifier', 'denitrifier'): 'nitrogen cycle: nitrifiers produce NO3- consumed by denitrifiers',
('aerobic_heterotroph', 'fermenter'): 'O2 gradient: aerobes deplete O2, creating anoxic niche for fermenters',
('fermenter', 'iron_reducer'): 'cross-feeding: fermenters produce organic acids as e-donors for Fe reduction',
('fermenter', 'sulfate_reducer'): 'cross-feeding: fermenters produce H2/acetate for sulfate reduction',
('predator', 'aerobic_heterotroph'): 'predation: Bdellovibrio preys on Gram-negative heterotrophs',
}
print(f"Guild map: {len(GENUS_GUILD)} genera in {len(GUILD_MAP)} guilds")
print(f"Interaction rules: {len(GUILD_INTERACTIONS)} known guild-guild interactions")
Guild map: 53 genera in 11 guilds Interaction rules: 11 known guild-guild interactions
2. Well-by-Well Hotspot Profiles¶
For each well, show the top genera, their guilds, and the guild composition. Then identify which metabolic interactions are possible at each location.
In [3]:
# Build guild abundance per well
guild_well = pd.DataFrame(0.0, index=WELL_ORDER, columns=sorted(GUILD_MAP.keys()))
for well in WELL_ORDER:
wdata = genus_well[genus_well['location'] == well]
for _, row in wdata.iterrows():
guild = GENUS_GUILD.get(row['genus'])
if guild:
guild_well.loc[well, guild] += row['rel_pct']
# Print hotspot profile for each well
hotspot_names = {
'SSO-U1': 'Iron Reduction Zone',
'SSO-U2': 'Sulfate Reduction Zone',
'SSO-U3': 'Plume Entry (Fe/N Oxidation)',
'SSO-M4': 'Methanotrophy/Sulfur Oxidation',
'SSO-M5': 'Denitrification Hotspot (Mixing Zone)',
'SSO-M6': 'Anaerobic Core (Plume Center)',
'SSO-L7': 'Plume Corridor Terminus',
'SSO-L8': 'Aerobic Heterotrophy Zone',
'SSO-L9': 'Fermentation Terminus',
}
all_profiles = []
for well in WELL_ORDER:
wdata = genus_well[genus_well['location'] == well].sort_values('rel_pct', ascending=False)
top15 = wdata.head(15)
print(f"\n{'='*70}")
print(f" {well} — {hotspot_names[well]}")
print(f"{'='*70}")
# Guild composition
guilds = guild_well.loc[well].sort_values(ascending=False)
guilds_present = guilds[guilds > 0]
print(f"\n Guild composition (annotated genera only):")
for guild, pct in guilds_present.items():
print(f" {guild:<25} {pct:>5.2f}%")
# Top genera with guilds
print(f"\n Top 15 genera:")
print(f" {'Genus':<35} {'%':>6} {'Guild':<25}")
print(f" {'-'*70}")
for _, row in top15.iterrows():
guild = GENUS_GUILD.get(row['genus'], '—')
print(f" {row['genus']:<35} {row['rel_pct']:>5.2f}% {guild:<25}")
# Identify active interactions at this well
active_guilds = set(guilds_present.index)
interactions = []
for (g1, g2), desc in GUILD_INTERACTIONS.items():
if g1 in active_guilds and g2 in active_guilds:
strength = min(guilds_present[g1], guilds_present[g2])
interactions.append((g1, g2, desc, strength))
if interactions:
interactions.sort(key=lambda x: -x[3])
print(f"\n Inferred metabolic interactions:")
for g1, g2, desc, strength in interactions:
print(f" {g1} ↔ {g2} ({strength:.2f}%)")
print(f" → {desc}")
for _, row in top15.iterrows():
all_profiles.append({
'well': well, 'genus': row['genus'],
'rel_pct': row['rel_pct'], 'guild': GENUS_GUILD.get(row['genus'], 'unassigned')
})
pd.DataFrame(all_profiles).to_csv(DATA / 'hotspot_profiles.csv', index=False)
guild_well.to_csv(DATA / 'guild_composition.csv')
======================================================================
SSO-U1 — Iron Reduction Zone
======================================================================
Guild composition (annotated genera only):
aerobic_heterotroph 9.63%
fermenter 2.83%
denitrifier 2.79%
iron_reducer 2.34%
sulfur_oxidizer 1.25%
methanotroph 0.73%
sulfate_reducer 0.54%
syntroph 0.48%
nitrifier 0.46%
predator 0.31%
iron_oxidizer 0.05%
Top 15 genera:
Genus % Guild
----------------------------------------------------------------------
Massilia 3.12% aerobic_heterotroph
Anaeromyxobacter 2.23% iron_reducer
Arcobacter 1.15% sulfur_oxidizer
Pseudomonas 1.04% aerobic_heterotroph
Candidatus Accumulibacter 0.98% —
Porphyrobacter 0.91% —
Spirochaeta 0.91% fermenter
Terrimonas 0.89% aerobic_heterotroph
Duganella 0.82% aerobic_heterotroph
Zoogloea 0.82% denitrifier
Acinetobacter 0.77% aerobic_heterotroph
Trichococcus 0.75% fermenter
Candidatus Methanoperedens 0.73% methanotroph
Methyloversatilis 0.70% denitrifier
Exiguobacterium 0.68% —
Inferred metabolic interactions:
aerobic_heterotroph ↔ fermenter (2.83%)
→ O2 gradient: aerobes deplete O2, creating anoxic niche for fermenters
denitrifier ↔ iron_reducer (2.34%)
→ sequential: denitrifiers consume NO3-, creating conditions for Fe reduction
fermenter ↔ iron_reducer (2.34%)
→ cross-feeding: fermenters produce organic acids as e-donors for Fe reduction
sulfur_oxidizer ↔ sulfate_reducer (0.54%)
→ sulfur cycle: oxidizers produce SO4, reducers regenerate H2S
fermenter ↔ sulfate_reducer (0.54%)
→ cross-feeding: fermenters produce H2/acetate for sulfate reduction
fermenter ↔ syntroph (0.48%)
→ cross-feeding: fermenters produce organic acids consumed by syntrophs
syntroph ↔ sulfate_reducer (0.48%)
→ syntrophic: syntrophs produce H2 consumed by sulfate reducers
syntroph ↔ methanotroph (0.48%)
→ syntrophic: H2/formate coupling in anaerobic methane oxidation
nitrifier ↔ denitrifier (0.46%)
→ nitrogen cycle: nitrifiers produce NO3- consumed by denitrifiers
predator ↔ aerobic_heterotroph (0.31%)
→ predation: Bdellovibrio preys on Gram-negative heterotrophs
iron_oxidizer ↔ iron_reducer (0.05%)
→ iron cycle: oxidizers produce Fe3+, reducers regenerate Fe2+
======================================================================
SSO-U2 — Sulfate Reduction Zone
======================================================================
Guild composition (annotated genera only):
aerobic_heterotroph 6.45%
fermenter 2.91%
denitrifier 1.79%
iron_reducer 1.45%
syntroph 1.26%
sulfate_reducer 1.18%
methanotroph 0.87%
sulfur_oxidizer 0.80%
nitrifier 0.73%
iron_oxidizer 0.09%
predator 0.07%
Top 15 genera:
Genus % Guild
----------------------------------------------------------------------
Spirochaeta 1.46% fermenter
Anaeromyxobacter 1.45% iron_reducer
BSV13 0.98% —
Afipia 0.92% aerobic_heterotroph
Candidatus Methanoperedens 0.86% methanotroph
Candidatus Solibacter 0.83% aerobic_heterotroph
Desulfosporosinus 0.82% sulfate_reducer
Bradyrhizobium 0.78% —
Terrimonas 0.70% aerobic_heterotroph
Arcobacter 0.70% sulfur_oxidizer
Gordonia 0.65% aerobic_heterotroph
Mesorhizobium 0.64% —
GOUTA6 0.64% —
Candidatus Cloacimonas 0.62% syntroph
Defluviicoccus 0.60% —
Inferred metabolic interactions:
aerobic_heterotroph ↔ fermenter (2.91%)
→ O2 gradient: aerobes deplete O2, creating anoxic niche for fermenters
denitrifier ↔ iron_reducer (1.45%)
→ sequential: denitrifiers consume NO3-, creating conditions for Fe reduction
fermenter ↔ iron_reducer (1.45%)
→ cross-feeding: fermenters produce organic acids as e-donors for Fe reduction
fermenter ↔ syntroph (1.26%)
→ cross-feeding: fermenters produce organic acids consumed by syntrophs
syntroph ↔ sulfate_reducer (1.18%)
→ syntrophic: syntrophs produce H2 consumed by sulfate reducers
fermenter ↔ sulfate_reducer (1.18%)
→ cross-feeding: fermenters produce H2/acetate for sulfate reduction
syntroph ↔ methanotroph (0.87%)
→ syntrophic: H2/formate coupling in anaerobic methane oxidation
sulfur_oxidizer ↔ sulfate_reducer (0.80%)
→ sulfur cycle: oxidizers produce SO4, reducers regenerate H2S
nitrifier ↔ denitrifier (0.73%)
→ nitrogen cycle: nitrifiers produce NO3- consumed by denitrifiers
iron_oxidizer ↔ iron_reducer (0.09%)
→ iron cycle: oxidizers produce Fe3+, reducers regenerate Fe2+
predator ↔ aerobic_heterotroph (0.07%)
→ predation: Bdellovibrio preys on Gram-negative heterotrophs
======================================================================
SSO-U3 — Plume Entry (Fe/N Oxidation)
======================================================================
Guild composition (annotated genera only):
denitrifier 6.51%
aerobic_heterotroph 4.59%
iron_oxidizer 2.83%
nitrifier 2.34%
iron_reducer 2.08%
fermenter 1.96%
sulfate_reducer 0.77%
syntroph 0.51%
sulfur_oxidizer 0.35%
methanotroph 0.27%
predator 0.04%
Top 15 genera:
Genus % Guild
----------------------------------------------------------------------
Rhodanobacter 5.80% denitrifier
Sideroxydans 2.66% iron_oxidizer
Anaeromyxobacter 1.97% iron_reducer
Rhizomicrobium 1.82% aerobic_heterotroph
Spirochaeta 1.79% fermenter
Candidatus Nitrosotalea 1.61% nitrifier
Occallatibacter 1.05% —
Candidatus Solibacter 0.96% aerobic_heterotroph
Oligotropha 0.94% —
Burkholderia-Caballeronia-Paraburkholderia 0.82% —
Desulfobacca 0.64% sulfate_reducer
Pseudolabrys 0.61% —
Candidatus Omnitrophus 0.58% aerobic_heterotroph
GOUTA6 0.55% —
BIyi10 0.53% —
Inferred metabolic interactions:
nitrifier ↔ denitrifier (2.34%)
→ nitrogen cycle: nitrifiers produce NO3- consumed by denitrifiers
denitrifier ↔ iron_reducer (2.08%)
→ sequential: denitrifiers consume NO3-, creating conditions for Fe reduction
iron_oxidizer ↔ iron_reducer (2.08%)
→ iron cycle: oxidizers produce Fe3+, reducers regenerate Fe2+
aerobic_heterotroph ↔ fermenter (1.96%)
→ O2 gradient: aerobes deplete O2, creating anoxic niche for fermenters
fermenter ↔ iron_reducer (1.96%)
→ cross-feeding: fermenters produce organic acids as e-donors for Fe reduction
fermenter ↔ sulfate_reducer (0.77%)
→ cross-feeding: fermenters produce H2/acetate for sulfate reduction
fermenter ↔ syntroph (0.51%)
→ cross-feeding: fermenters produce organic acids consumed by syntrophs
syntroph ↔ sulfate_reducer (0.51%)
→ syntrophic: syntrophs produce H2 consumed by sulfate reducers
sulfur_oxidizer ↔ sulfate_reducer (0.35%)
→ sulfur cycle: oxidizers produce SO4, reducers regenerate H2S
syntroph ↔ methanotroph (0.27%)
→ syntrophic: H2/formate coupling in anaerobic methane oxidation
predator ↔ aerobic_heterotroph (0.04%)
→ predation: Bdellovibrio preys on Gram-negative heterotrophs
======================================================================
SSO-M4 — Methanotrophy/Sulfur Oxidation
======================================================================
Guild composition (annotated genera only):
aerobic_heterotroph 6.94%
fermenter 3.64%
denitrifier 2.74%
sulfur_oxidizer 1.85%
syntroph 1.38%
nitrifier 1.05%
iron_reducer 1.03%
sulfate_reducer 0.66%
methanotroph 0.55%
iron_oxidizer 0.48%
predator 0.38%
Top 15 genera:
Genus % Guild
----------------------------------------------------------------------
Spirochaeta 1.44% fermenter
Arcobacter 1.18% sulfur_oxidizer
Anoxybacillus 1.13% fermenter
Candidatus Omnitrophus 1.10% aerobic_heterotroph
Methyloversatilis 1.06% denitrifier
Anaeromyxobacter 1.01% iron_reducer
Pseudomonas 0.94% aerobic_heterotroph
Bradyrhizobium 0.85% —
Acinetobacter 0.85% aerobic_heterotroph
Rhodanobacter 0.81% denitrifier
Terrimonas 0.77% aerobic_heterotroph
Candidatus Cloacimonas 0.75% syntroph
Thiobacillus 0.67% sulfur_oxidizer
Sphingomonas 0.66% aerobic_heterotroph
OLB12 0.65% —
Inferred metabolic interactions:
aerobic_heterotroph ↔ fermenter (3.64%)
→ O2 gradient: aerobes deplete O2, creating anoxic niche for fermenters
fermenter ↔ syntroph (1.38%)
→ cross-feeding: fermenters produce organic acids consumed by syntrophs
nitrifier ↔ denitrifier (1.05%)
→ nitrogen cycle: nitrifiers produce NO3- consumed by denitrifiers
denitrifier ↔ iron_reducer (1.03%)
→ sequential: denitrifiers consume NO3-, creating conditions for Fe reduction
fermenter ↔ iron_reducer (1.03%)
→ cross-feeding: fermenters produce organic acids as e-donors for Fe reduction
syntroph ↔ sulfate_reducer (0.66%)
→ syntrophic: syntrophs produce H2 consumed by sulfate reducers
sulfur_oxidizer ↔ sulfate_reducer (0.66%)
→ sulfur cycle: oxidizers produce SO4, reducers regenerate H2S
fermenter ↔ sulfate_reducer (0.66%)
→ cross-feeding: fermenters produce H2/acetate for sulfate reduction
syntroph ↔ methanotroph (0.55%)
→ syntrophic: H2/formate coupling in anaerobic methane oxidation
iron_oxidizer ↔ iron_reducer (0.48%)
→ iron cycle: oxidizers produce Fe3+, reducers regenerate Fe2+
predator ↔ aerobic_heterotroph (0.38%)
→ predation: Bdellovibrio preys on Gram-negative heterotrophs
======================================================================
SSO-M5 — Denitrification Hotspot (Mixing Zone)
======================================================================
Guild composition (annotated genera only):
denitrifier 7.73%
aerobic_heterotroph 6.82%
fermenter 3.26%
iron_reducer 0.84%
nitrifier 0.80%
sulfate_reducer 0.73%
sulfur_oxidizer 0.69%
syntroph 0.62%
methanotroph 0.22%
predator 0.16%
iron_oxidizer 0.05%
Top 15 genera:
Genus % Guild
----------------------------------------------------------------------
Rhodanobacter 5.15% denitrifier
Spirochaeta 2.06% fermenter
Gaiella 1.08% aerobic_heterotroph
Herbaspirillum 0.95% —
Castellaniella 0.90% denitrifier
Anaeromyxobacter 0.69% iron_reducer
Candidatus Solibacter 0.68% aerobic_heterotroph
Oligotropha 0.68% —
Arcobacter 0.67% sulfur_oxidizer
Occallatibacter 0.64% —
Massilia 0.63% aerobic_heterotroph
Anoxybacillus 0.62% fermenter
Sphingomonas 0.62% aerobic_heterotroph
Rhizomicrobium 0.60% aerobic_heterotroph
Gordonia 0.58% aerobic_heterotroph
Inferred metabolic interactions:
aerobic_heterotroph ↔ fermenter (3.26%)
→ O2 gradient: aerobes deplete O2, creating anoxic niche for fermenters
denitrifier ↔ iron_reducer (0.84%)
→ sequential: denitrifiers consume NO3-, creating conditions for Fe reduction
fermenter ↔ iron_reducer (0.84%)
→ cross-feeding: fermenters produce organic acids as e-donors for Fe reduction
nitrifier ↔ denitrifier (0.80%)
→ nitrogen cycle: nitrifiers produce NO3- consumed by denitrifiers
fermenter ↔ sulfate_reducer (0.73%)
→ cross-feeding: fermenters produce H2/acetate for sulfate reduction
sulfur_oxidizer ↔ sulfate_reducer (0.69%)
→ sulfur cycle: oxidizers produce SO4, reducers regenerate H2S
fermenter ↔ syntroph (0.62%)
→ cross-feeding: fermenters produce organic acids consumed by syntrophs
syntroph ↔ sulfate_reducer (0.62%)
→ syntrophic: syntrophs produce H2 consumed by sulfate reducers
syntroph ↔ methanotroph (0.22%)
→ syntrophic: H2/formate coupling in anaerobic methane oxidation
predator ↔ aerobic_heterotroph (0.16%)
→ predation: Bdellovibrio preys on Gram-negative heterotrophs
iron_oxidizer ↔ iron_reducer (0.05%)
→ iron cycle: oxidizers produce Fe3+, reducers regenerate Fe2+
======================================================================
SSO-M6 — Anaerobic Core (Plume Center)
======================================================================
Guild composition (annotated genera only):
aerobic_heterotroph 8.05%
denitrifier 2.58%
fermenter 2.26%
syntroph 1.12%
sulfate_reducer 0.84%
iron_reducer 0.54%
sulfur_oxidizer 0.37%
nitrifier 0.33%
methanotroph 0.06%
predator 0.05%
iron_oxidizer 0.01%
Top 15 genera:
Genus % Guild
----------------------------------------------------------------------
Rhizomicrobium 3.65% aerobic_heterotroph
Spirochaeta 2.00% fermenter
Rhodanobacter 1.88% denitrifier
Candidatus Solibacter 1.73% aerobic_heterotroph
Candidatus Omnitrophus 1.17% aerobic_heterotroph
Occallatibacter 0.97% —
Syntrophus 0.96% syntroph
Desulfurivibrio 0.81% —
Desulfobacca 0.77% sulfate_reducer
Anaeromyxobacter 0.53% iron_reducer
Castellaniella 0.43% denitrifier
Ignavibacterium 0.41% —
Comamonas 0.40% aerobic_heterotroph
Truepera 0.39% —
Ramlibacter 0.39% —
Inferred metabolic interactions:
aerobic_heterotroph ↔ fermenter (2.26%)
→ O2 gradient: aerobes deplete O2, creating anoxic niche for fermenters
fermenter ↔ syntroph (1.12%)
→ cross-feeding: fermenters produce organic acids consumed by syntrophs
syntroph ↔ sulfate_reducer (0.84%)
→ syntrophic: syntrophs produce H2 consumed by sulfate reducers
fermenter ↔ sulfate_reducer (0.84%)
→ cross-feeding: fermenters produce H2/acetate for sulfate reduction
denitrifier ↔ iron_reducer (0.54%)
→ sequential: denitrifiers consume NO3-, creating conditions for Fe reduction
fermenter ↔ iron_reducer (0.54%)
→ cross-feeding: fermenters produce organic acids as e-donors for Fe reduction
sulfur_oxidizer ↔ sulfate_reducer (0.37%)
→ sulfur cycle: oxidizers produce SO4, reducers regenerate H2S
nitrifier ↔ denitrifier (0.33%)
→ nitrogen cycle: nitrifiers produce NO3- consumed by denitrifiers
syntroph ↔ methanotroph (0.06%)
→ syntrophic: H2/formate coupling in anaerobic methane oxidation
predator ↔ aerobic_heterotroph (0.05%)
→ predation: Bdellovibrio preys on Gram-negative heterotrophs
iron_oxidizer ↔ iron_reducer (0.01%)
→ iron cycle: oxidizers produce Fe3+, reducers regenerate Fe2+
======================================================================
SSO-L7 — Plume Corridor Terminus
======================================================================
Guild composition (annotated genera only):
aerobic_heterotroph 5.27%
denitrifier 3.98%
fermenter 2.81%
iron_reducer 1.69%
sulfate_reducer 0.87%
syntroph 0.82%
methanotroph 0.59%
nitrifier 0.40%
sulfur_oxidizer 0.40%
iron_oxidizer 0.01%
predator 0.01%
Top 15 genera:
Genus % Guild
----------------------------------------------------------------------
Spirochaeta 2.43% fermenter
Rhodanobacter 2.33% denitrifier
Anaeromyxobacter 1.69% iron_reducer
Rhizomicrobium 1.03% aerobic_heterotroph
Chujaibacter 0.86% aerobic_heterotroph
Methyloversatilis 0.78% denitrifier
Candidatus Solibacter 0.74% aerobic_heterotroph
Occallatibacter 0.65% —
Candidatus Methanoperedens 0.59% methanotroph
Desulfosporosinus 0.54% sulfate_reducer
Candidatus Omnitrophus 0.54% aerobic_heterotroph
Sphingomonas 0.41% aerobic_heterotroph
HSB OF53-F07 0.38% —
Candidatus Cloacimonas 0.38% syntroph
Gaiella 0.36% aerobic_heterotroph
Inferred metabolic interactions:
aerobic_heterotroph ↔ fermenter (2.81%)
→ O2 gradient: aerobes deplete O2, creating anoxic niche for fermenters
denitrifier ↔ iron_reducer (1.69%)
→ sequential: denitrifiers consume NO3-, creating conditions for Fe reduction
fermenter ↔ iron_reducer (1.69%)
→ cross-feeding: fermenters produce organic acids as e-donors for Fe reduction
fermenter ↔ sulfate_reducer (0.87%)
→ cross-feeding: fermenters produce H2/acetate for sulfate reduction
fermenter ↔ syntroph (0.82%)
→ cross-feeding: fermenters produce organic acids consumed by syntrophs
syntroph ↔ sulfate_reducer (0.82%)
→ syntrophic: syntrophs produce H2 consumed by sulfate reducers
syntroph ↔ methanotroph (0.59%)
→ syntrophic: H2/formate coupling in anaerobic methane oxidation
nitrifier ↔ denitrifier (0.40%)
→ nitrogen cycle: nitrifiers produce NO3- consumed by denitrifiers
sulfur_oxidizer ↔ sulfate_reducer (0.40%)
→ sulfur cycle: oxidizers produce SO4, reducers regenerate H2S
iron_oxidizer ↔ iron_reducer (0.01%)
→ iron cycle: oxidizers produce Fe3+, reducers regenerate Fe2+
predator ↔ aerobic_heterotroph (0.01%)
→ predation: Bdellovibrio preys on Gram-negative heterotrophs
======================================================================
SSO-L8 — Aerobic Heterotrophy Zone
======================================================================
Guild composition (annotated genera only):
aerobic_heterotroph 11.46%
fermenter 2.28%
denitrifier 2.02%
iron_reducer 1.25%
syntroph 1.20%
sulfur_oxidizer 0.86%
nitrifier 0.66%
methanotroph 0.59%
sulfate_reducer 0.54%
predator 0.06%
iron_oxidizer 0.04%
Top 15 genera:
Genus % Guild
----------------------------------------------------------------------
Rhizomicrobium 1.74% aerobic_heterotroph
Candidatus Solibacter 1.41% aerobic_heterotroph
Anaeromyxobacter 1.24% iron_reducer
Comamonas 1.23% aerobic_heterotroph
Spirochaeta 1.14% fermenter
Pseudomonas 1.02% aerobic_heterotroph
Candidatus Omnitrophus 0.89% aerobic_heterotroph
Syntrophus 0.82% syntroph
Ferruginibacter 0.81% aerobic_heterotroph
Paenarthrobacter 0.75% aerobic_heterotroph
Arcobacter 0.75% sulfur_oxidizer
Terrimonas 0.73% aerobic_heterotroph
Rhodanobacter 0.68% denitrifier
Sphingomonas 0.67% aerobic_heterotroph
Afipia 0.61% aerobic_heterotroph
Inferred metabolic interactions:
aerobic_heterotroph ↔ fermenter (2.28%)
→ O2 gradient: aerobes deplete O2, creating anoxic niche for fermenters
denitrifier ↔ iron_reducer (1.25%)
→ sequential: denitrifiers consume NO3-, creating conditions for Fe reduction
fermenter ↔ iron_reducer (1.25%)
→ cross-feeding: fermenters produce organic acids as e-donors for Fe reduction
fermenter ↔ syntroph (1.20%)
→ cross-feeding: fermenters produce organic acids consumed by syntrophs
nitrifier ↔ denitrifier (0.66%)
→ nitrogen cycle: nitrifiers produce NO3- consumed by denitrifiers
syntroph ↔ methanotroph (0.59%)
→ syntrophic: H2/formate coupling in anaerobic methane oxidation
syntroph ↔ sulfate_reducer (0.54%)
→ syntrophic: syntrophs produce H2 consumed by sulfate reducers
sulfur_oxidizer ↔ sulfate_reducer (0.54%)
→ sulfur cycle: oxidizers produce SO4, reducers regenerate H2S
fermenter ↔ sulfate_reducer (0.54%)
→ cross-feeding: fermenters produce H2/acetate for sulfate reduction
predator ↔ aerobic_heterotroph (0.06%)
→ predation: Bdellovibrio preys on Gram-negative heterotrophs
iron_oxidizer ↔ iron_reducer (0.04%)
→ iron cycle: oxidizers produce Fe3+, reducers regenerate Fe2+
======================================================================
SSO-L9 — Fermentation Terminus
======================================================================
Guild composition (annotated genera only):
aerobic_heterotroph 8.19%
fermenter 4.97%
denitrifier 2.34%
iron_reducer 1.64%
syntroph 1.31%
nitrifier 1.09%
sulfur_oxidizer 0.73%
predator 0.70%
sulfate_reducer 0.33%
iron_oxidizer 0.31%
methanotroph 0.04%
Top 15 genera:
Genus % Guild
----------------------------------------------------------------------
Paenisporosarcina 3.18% fermenter
Anaeromyxobacter 1.51% iron_reducer
Sphingomonas 1.31% aerobic_heterotroph
Spirochaeta 0.97% fermenter
Zoogloea 0.95% denitrifier
Syntrophus 0.93% syntroph
MND1 0.90% nitrifier
Acinetobacter 0.88% aerobic_heterotroph
Rhodanobacter 0.76% denitrifier
Pseudomonas 0.71% aerobic_heterotroph
Bdellovibrio 0.70% predator
Klebsiella 0.69% —
Gordonia 0.69% aerobic_heterotroph
Terrimonas 0.66% aerobic_heterotroph
Gaiella 0.66% aerobic_heterotroph
Inferred metabolic interactions:
aerobic_heterotroph ↔ fermenter (4.97%)
→ O2 gradient: aerobes deplete O2, creating anoxic niche for fermenters
denitrifier ↔ iron_reducer (1.64%)
→ sequential: denitrifiers consume NO3-, creating conditions for Fe reduction
fermenter ↔ iron_reducer (1.64%)
→ cross-feeding: fermenters produce organic acids as e-donors for Fe reduction
fermenter ↔ syntroph (1.31%)
→ cross-feeding: fermenters produce organic acids consumed by syntrophs
nitrifier ↔ denitrifier (1.09%)
→ nitrogen cycle: nitrifiers produce NO3- consumed by denitrifiers
predator ↔ aerobic_heterotroph (0.70%)
→ predation: Bdellovibrio preys on Gram-negative heterotrophs
syntroph ↔ sulfate_reducer (0.33%)
→ syntrophic: syntrophs produce H2 consumed by sulfate reducers
sulfur_oxidizer ↔ sulfate_reducer (0.33%)
→ sulfur cycle: oxidizers produce SO4, reducers regenerate H2S
fermenter ↔ sulfate_reducer (0.33%)
→ cross-feeding: fermenters produce H2/acetate for sulfate reduction
iron_oxidizer ↔ iron_reducer (0.31%)
→ iron cycle: oxidizers produce Fe3+, reducers regenerate Fe2+
syntroph ↔ methanotroph (0.04%)
→ syntrophic: H2/formate coupling in anaerobic methane oxidation
3. Guild Composition Across the Grid¶
In [4]:
# Stacked bar: guild composition per well
guild_order = ['denitrifier', 'nitrifier', 'iron_reducer', 'iron_oxidizer',
'sulfate_reducer', 'sulfur_oxidizer', 'syntroph', 'methanotroph',
'fermenter', 'aerobic_heterotroph', 'predator']
guild_colors = {
'denitrifier': '#1565C0', 'nitrifier': '#42A5F5',
'iron_reducer': '#E65100', 'iron_oxidizer': '#FF9800',
'sulfate_reducer': '#4A148C', 'sulfur_oxidizer': '#CE93D8',
'syntroph': '#2E7D32', 'methanotroph': '#81C784',
'fermenter': '#C62828', 'aerobic_heterotroph': '#90CAF9',
'predator': '#795548',
}
fig, ax = plt.subplots(figsize=(12, 6))
bottom = np.zeros(9)
x = np.arange(9)
for guild in guild_order:
vals = guild_well.loc[WELL_ORDER, guild].values.astype(float)
if vals.sum() > 0:
ax.bar(x, vals, bottom=bottom, label=guild.replace('_', ' ').title(),
color=guild_colors[guild], edgecolor='white', linewidth=0.5)
bottom += vals
ax.set_xticks(x)
ax.set_xticklabels([w.replace('SSO-', '') + '\n' + hotspot_names['SSO-' + w.replace('SSO-','')].split('(')[0].strip()
if 'SSO-' in w else w.replace('SSO-','')
for w in WELL_ORDER], fontsize=8, rotation=0)
# Simpler labels
ax.set_xticks(x)
labels = [f"{w.replace('SSO-','')}" for w in WELL_ORDER]
ax.set_xticklabels(labels, fontsize=10)
ax.set_ylabel('Relative Abundance (%)', fontsize=11)
ax.set_title('Metabolic Guild Composition Across SSO Wells\n(genus-level annotation)', fontsize=13)
ax.legend(bbox_to_anchor=(1.02, 1), loc='upper left', fontsize=8)
plt.tight_layout()
plt.savefig(FIG / 'guild_composition_bars.png', dpi=150, bbox_inches='tight')
plt.show()
print("Saved: figures/guild_composition_bars.png")
Saved: figures/guild_composition_bars.png
In [5]:
# Guild co-occurrence heatmap: which guilds appear together across wells?
# Spearman correlation of guild abundances across the 9 wells
guild_present = guild_well[guild_order].loc[WELL_ORDER]
guild_present = guild_present.loc[:, guild_present.sum() > 0] # drop empty guilds
guild_corr = guild_present.corr(method='spearman')
fig, ax = plt.subplots(figsize=(10, 8))
mask = np.triu(np.ones_like(guild_corr, dtype=bool), k=1)
sns.heatmap(guild_corr, mask=mask, annot=True, fmt='.2f', cmap='RdBu_r', center=0,
vmin=-1, vmax=1, square=True, linewidths=0.5, ax=ax,
xticklabels=[g.replace('_', '\n') for g in guild_corr.columns],
yticklabels=[g.replace('_', '\n') for g in guild_corr.index])
ax.set_title('Guild Co-occurrence Across Wells\n(Spearman correlation, n=9)', fontsize=12)
plt.tight_layout()
plt.savefig(FIG / 'guild_cooccurrence.png', dpi=150, bbox_inches='tight')
plt.show()
print("Saved: figures/guild_cooccurrence.png")
# Highlight strong co-occurrences and anti-correlations
print("\nStrong guild co-occurrences (|rho| > 0.5):")
for i, g1 in enumerate(guild_corr.columns):
for j, g2 in enumerate(guild_corr.columns):
if i < j:
rho = guild_corr.loc[g1, g2]
if abs(rho) > 0.5:
direction = "co-occur" if rho > 0 else "exclude"
interaction = GUILD_INTERACTIONS.get((g1, g2)) or GUILD_INTERACTIONS.get((g2, g1)) or "no known direct interaction"
print(f" {g1} × {g2}: rho={rho:+.2f} ({direction})")
print(f" Known: {interaction}")
Saved: figures/guild_cooccurrence.png
Strong guild co-occurrences (|rho| > 0.5):
denitrifier × syntroph: rho=-0.67 (exclude)
Known: no known direct interaction
nitrifier × iron_oxidizer: rho=+0.95 (co-occur)
Known: no known direct interaction
sulfate_reducer × aerobic_heterotroph: rho=-0.75 (exclude)
Known: no known direct interaction
sulfate_reducer × predator: rho=-0.65 (exclude)
Known: no known direct interaction
sulfur_oxidizer × fermenter: rho=+0.57 (co-occur)
Known: no known direct interaction
sulfur_oxidizer × aerobic_heterotroph: rho=+0.58 (co-occur)
Known: no known direct interaction
sulfur_oxidizer × predator: rho=+0.68 (co-occur)
Known: no known direct interaction
syntroph × fermenter: rho=+0.55 (co-occur)
Known: cross-feeding: fermenters produce organic acids consumed by syntrophs
fermenter × predator: rho=+0.85 (co-occur)
Known: no known direct interaction
aerobic_heterotroph × predator: rho=+0.52 (co-occur)
Known: predation: Bdellovibrio preys on Gram-negative heterotrophs