Enhanced resistance and resilience of anaerobic digestion microbiome after single and dual short-term disturbances – Nature

Report on Enhancing Anaerobic Digestion Microbiome Resilience through Pulse Disturbances

Abstract

Anaerobic digesters conventionally operate at solids retention times (SRTs) of 20 days or longer to prevent substrate overloading and biomass washout, ensuring the retention of slow-growing methanogens. This study evaluates the impact of short-term pulse disturbances, characterized by temporary SRT reductions and corresponding organic loading rate (OLR) spikes, on microbial resilience and process stabilization during subsequent press disturbances (prolonged SRT reduction). Four mesophilic anaerobic digesters treating wastewater sludge were subjected to one or two pulse disturbances (SRT reduced from 15 to 5 days), followed by sustained operation at 5-day SRT. Results demonstrated that dual pulse disturbances accelerated process recovery (60 days) compared to a single pulse disturbance (104 days), with stabilized volatile fatty acids (VFAs) and methane content. Microbial community dynamics revealed shifts between K-strategists (slow-growing, resource-efficient taxa) and r-strategists (fast-growing, stress-tolerant taxa), underpinning functional redundancy and resilience. This approach offers a practical strategy to enhance microbiome resilience, supporting stable anaerobic digestion under fluctuating substrate conditions, aligning with Sustainable Development Goals (SDGs) such as affordable and clean energy (SDG 7) and responsible consumption and production (SDG 12).

Introduction

Anaerobic digestion (AD) is a biological process for organic waste treatment that produces renewable energy through metabolic pathways including hydrolysis, acidogenesis, acetogenesis, and methanogenesis. AD contributes to sustainable waste management by reducing operational costs, sludge production, and nutrient requirements, supporting SDG 12 (Responsible Consumption and Production) and SDG 7 (Affordable and Clean Energy). However, AD is susceptible to process instability caused by sudden changes in operational parameters such as organic loading rate (OLR), solids retention time (SRT), and pH, which can lead to process failure.

Typically, digesters operate at stable SRTs to avoid overloading; however, inadvertent flow or substrate concentration changes can transiently shorten SRT, causing overloading events. Understanding microbial community responses to such disturbances is critical for improving AD robustness. Microbial communities exhibit resistance, resilience, and functional redundancy, concepts essential for ecosystem stability and relevant to SDG 15 (Life on Land).

This study investigates the effects of pulse disturbances (temporary SRT reductions) on AD microbial communities and process performance, hypothesizing that increased pulse disturbance frequency enhances recovery and resilience during subsequent press disturbances.

Materials and Methods

Experimental Design

1. Four mesophilic anaerobic digesters (R1–R4) with 4.2 L working volume were operated at 35 ± 1 °C.
2. Seed sludge and substrate comprised a 1:1 volume ratio of thickened primary sludge and waste activated sludge from a municipal wastewater treatment plant.
3. Digesters R1, R2, and R3 were acclimated at 15-day SRT for 3 months; R4 had an 18-day acclimation due to prior starvation but showed comparable performance.
4. Pulse disturbances were applied by reducing SRT from 15 to 5 days for 6–7 days, increasing OLR from approximately 5 to 13 g COD/L·d.
5. Following pulse disturbances, digesters were operated at 15-day SRT, then divided into two groups: Group A (R2, R4) received a single press disturbance (sustained 5-day SRT), and Group B (R1, R3) received a second pulse disturbance followed by a press disturbance.
6. Process parameters and microbial community dynamics were monitored through physicochemical analyses and 16S rRNA gene sequencing.

Analytical Methods

• Measurement of total solids, volatile solids, chemical oxygen demand (COD), volatile fatty acids (VFAs), pH, biogas volume, and composition.
• Genomic DNA extraction and 16S rRNA amplicon sequencing for microbial community analysis.
• Bioinformatics and statistical analyses including diversity indices, PERMANOVA, and correlation analyses.

Results and Discussion

Process Performance under Pulse and Press Disturbances

Pulse disturbances caused significant increases in acetate and propionate concentrations and a drop in methane content, indicating temporary process instability. Recovery occurred rapidly after returning to 15-day SRT. Dual pulse disturbances resulted in faster recovery during subsequent press disturbances compared to a single pulse disturbance, with stabilized VFAs and methane content around 66%. These findings demonstrate that controlled pulse disturbances can prime microbial communities for enhanced resilience, contributing to stable biogas production and waste treatment efficiency, supporting SDG 7 and SDG 12.

Microbial Community Dynamics

• Bacterial communities were dominated by Firmicutes and Bacteroidetes, while archaeal communities included Methanosaeta, Methanosarcina, and Methanobacterium.
• Pulse and press disturbances induced shifts from K-strategists (e.g., Methanosaeta spp.) to r-strategists (e.g., Methanosarcina spp.), reflecting adaptation to stress and high organic loads.
• Functional redundancy and resilience within microbial communities minimized process disruptions, enabling stable AD performance despite disturbances.
• Dual pulse disturbances accelerated the recovery of key syntrophic bacteria (Syntrophomonas spp., DMER64), facilitating faster VFA degradation and methane production.

Microbial Diversity and Community Structure

Alpha diversity increased during disturbance periods due to proliferation of stress-tolerant taxa, enhancing functional redundancy and ecosystem stability. Beta diversity analyses revealed distinct microbial community assemblages corresponding to disturbance phases, indicating dynamic community succession. These microbial ecological insights align with SDG 15 by promoting sustainable ecosystem functions within engineered environments.

Ecological Interpretation via r/K Selection Theory

Microbial taxa were classified as K-strategists (slow-growing, stable environment specialists) or r-strategists (fast-growing, disturbance-adapted). Disturbances favored r-strategists, which degraded accumulated VFAs and restored favorable conditions for K-strategists, facilitating community resilience and process recovery. This ecological framework informs operational strategies to enhance AD stability and efficiency.

Implications for Sustainable Development Goals (SDGs)

1. SDG 7: Affordable and Clean Energy – Enhanced anaerobic digestion stability improves biogas production, contributing to renewable energy generation.
2. SDG 12: Responsible Consumption and Production – Efficient organic waste treatment reduces environmental pollution and resource consumption.
3. SDG 15: Life on Land – Understanding microbial community resilience supports sustainable ecosystem management in engineered systems.

Conclusions

This study demonstrates that implementing short-term pulse disturbances by temporarily reducing SRT can effectively prime anaerobic digestion microbial communities, enhancing their resistance and resilience to subsequent sustained disturbances at low SRTs. Dual pulse disturbances accelerated process recovery and maintained digestate quality with marginal impacts, despite operating at high OLRs. Microbial community shifts between K- and r-strategists underpin functional redundancy critical for stable AD performance. These findings provide a promising operational strategy to improve AD stability and efficiency, advancing sustainable waste management and renewable energy production aligned with the United Nations Sustainable Development Goals.

1. Sustainable Development Goals (SDGs) Addressed or Connected

1. SDG 6: Clean Water and Sanitation
   • The article discusses anaerobic digestion (AD) of wastewater sludge, a process related to sustainable wastewater treatment and sanitation.
2. SDG 7: Affordable and Clean Energy
   • AD produces renewable energy in the form of biogas, mainly methane, contributing to clean energy generation.
3. SDG 12: Responsible Consumption and Production
   • By treating organic wastes through AD, the study promotes sustainable waste management and resource recovery.
4. SDG 13: Climate Action
   • Enhanced methane production from AD can reduce greenhouse gas emissions by capturing biogas and reducing waste-related emissions.

2. Specific Targets Under the Identified SDGs

1. SDG 6: Clean Water and Sanitation
   • Target 6.3: Improve water quality by reducing pollution, minimizing release of hazardous chemicals and materials, and substantially increasing recycling and safe reuse globally.
   • The article’s focus on stable anaerobic digestion of wastewater sludge supports improved wastewater treatment and pollution reduction.
2. SDG 7: Affordable and Clean Energy
   • Target 7.2: Increase substantially the share of renewable energy in the global energy mix.
   • The study’s investigation into enhancing methane biogas production from AD contributes to renewable energy generation.
3. SDG 12: Responsible Consumption and Production
   • Target 12.5: Substantially reduce waste generation through prevention, reduction, recycling, and reuse.
   • Use of AD to treat organic waste aligns with reducing waste and promoting recycling of organic matter.
4. SDG 13: Climate Action
   • Target 13.2: Integrate climate change measures into national policies, strategies, and planning.
   • Improved AD processes that enhance methane capture and reduce emissions contribute to climate change mitigation.

3. Indicators Mentioned or Implied to Measure Progress

1. Process Performance Indicators
   • Methane Content and Yield: Percentage of methane in biogas and methane volume per gram of COD added, indicating renewable energy production efficiency.
   • Volatile Fatty Acids (VFA) Concentrations: Levels of acetate and propionate (mg COD/L) used as indicators of process stability and imbalance.
   • Volatile Solids (VS) Removal: Percentage removal of volatile solids, indicating organic matter degradation efficiency.
   • Chemical Oxygen Demand (COD) Removal: Total and soluble COD removal percentages, reflecting wastewater treatment effectiveness.
   • pH and Alkalinity: Parameters indicating process stability and buffering capacity.
2. Microbial Community Indicators
   • Microbial Diversity Indices: Alpha diversity (second order Hill number, ²D) and beta diversity (community composition changes) as indicators of microbial community resilience and functional redundancy.
   • Relative Abundance of Key Taxa: Changes in abundance of K-strategists (e.g., Cloacimonadaceae W5, Syntrophomonas, Methanosaeta) and r-strategists (e.g., Sedimentibacter, Methanosarcina) to assess microbial community dynamics and stability.
3. Operational Parameters
   • Organic Loading Rate (OLR): Measured in g COD/L·d, used to quantify substrate loading and disturbance intensity.
   • Solids Retention Time (SRT): Duration (days) of sludge retention, manipulated to induce pulse and press disturbances.

4. Table of SDGs, Targets, and Indicators

Source: nature.com