Aerobic methanotrophs and the associated microbial network: resilience and stress response.

Microorganisms are a source, as well as a sink for methane, a potent primary greenhouse gas (GHG). Methane emissions would have been higher if not for the aerobic methane-oxidizers (methanotrophs) consuming the produced methane before being released into the atmosphere. These “low-affinity” methanotrophs thrive in niches where methane and oxygen availability overlap, and are of particular relevance in high methane-emitting environments (e.g., rice paddies, landfill covers, river sediments), whereas the “high-affinity” methanotrophs are responsible for consuming atmospheric methane at trace levels in well aerated soils. Although shown to be resilient to sporadic disturbances, less is known on how methanotrophs respond to recurring/compounded disturbances, and the role of the accompanying non-methanotrophs in modulating methanotrophic activity remains to be determined. Hence, the central hypothesis was: Methanotrophs are resilient to environmental disturbances, but recurring or compounded disturbances may have a cumulative effect, compromising methanotrophic activity, which is also modulated by interactions with the biotic environment. The hypothesis was addressed by microcosm- and mesocosm-based studies, capitalizing on stable isotopes, trace gas analytics, and state-of-the art molecular analyses of specific genes and gene transcripts

Response and resilience of methanotrophs to disturbances

Methanotrophic bacteria are the only known biological sink for the greenhouse gas methane. Therefore, methanotrophs play a key function in carbon cycling, an important biogeochemical process that affects global climate change. Yet, little is known of their vulnerability and resilience to disturbances. Driven by the gap of knowledge, this PhD thesis is a seminal study focusing on the recovery of methanotrophs from disturbances with respect to population dynamics, diversity and functioning. Two model disturbances were tested; disturbance-induced mortality and heat shock. While the former model disturbance represents a non-selective form of disturbance, the heat shock treatment may select for sub-populations of thermo-tolerant methanotrophs. Overall, methanotrophs are shown to be remarkably resilient to induced disturbances, compensating and even over-compensating for methane uptake during recovery. Type II methanotrophs, known to be present in high abundance as resting cells, appear to become more important during disturbances. Furthermore, the establishment and subsequent development of the methanotrophic community and activity were studied along a rice paddy chronosequence. With the influx of anthropogenic influences once a rice paddy is formed, the methanotrophic community structure is anticipated to undergo a dramatic change which in turn, may affect the activity. It appears that the young and ancient rice paddies do not show clear divergence, suggesting that the methane oxidizing community was soon established after a rice paddy is formed. However, the selection of the best adapted sub-population needs time. Accordingly, long term rice agriculture allows for higher methane uptake, and may select for a methanotroph sub-population that remains active. The predominant methanotrophs found in the Chinese rice paddies are type II, mainly Methylocystis species, and type Ib (RPC-1). However, type Ib seems to be the active dominant sub-population. This and previous studies suggest specific adaptation of type Ib to rice paddy environments. Interestingly, novel sequences phylogenetically grouped between pmoA and amoA were detected. Overall, paddy soil methanotrophs are not only able to recover from disturbances, but are apparently showing specific adaptation to rice paddy environments, demonstrating their resilience in face of perturbation

Response and resilience of methanotrophs to disturbances

Methanotrophic bacteria are the only known biological sink for the greenhouse gas methane. Therefore, methanotrophs play a key function in carbon cycling, an important biogeochemical process that affects global climate change. Yet, little is known of their vulnerability and resilience to disturbances. Driven by the gap of knowledge, this PhD thesis is a seminal study focusing on the recovery of methanotrophs from disturbances with respect to population dynamics, diversity and functioning. Two model disturbances were tested; disturbance-induced mortality and heat shock. While the former model disturbance represents a non-selective form of disturbance, the heat shock treatment may select for sub-populations of thermo-tolerant methanotrophs. Overall, methanotrophs are shown to be remarkably resilient to induced disturbances, compensating and even over-compensating for methane uptake during recovery. Type II methanotrophs, known to be present in high abundance as resting cells, appear to become more important during disturbances. Furthermore, the establishment and subsequent development of the methanotrophic community and activity were studied along a rice paddy chronosequence. With the influx of anthropogenic influences once a rice paddy is formed, the methanotrophic community structure is anticipated to undergo a dramatic change which in turn, may affect the activity. It appears that the young and ancient rice paddies do not show clear divergence, suggesting that the methane oxidizing community was soon established after a rice paddy is formed. However, the selection of the best adapted sub-population needs time. Accordingly, long term rice agriculture allows for higher methane uptake, and may select for a methanotroph sub-population that remains active. The predominant methanotrophs found in the Chinese rice paddies are type II, mainly Methylocystis species, and type Ib (RPC-1). However, type Ib seems to be the active dominant sub-population. This and previous studies suggest specific adaptation of type Ib to rice paddy environments. Interestingly, novel sequences phylogenetically grouped between pmoA and amoA were detected. Overall, paddy soil methanotrophs are not only able to recover from disturbances, but are apparently showing specific adaptation to rice paddy environments, demonstrating their resilience in face of perturbation