Positive diversity-functioning relationships in model communities of methanotrophic bacteria

Methane emissions and microbial communities under differing flooding conditions and seasons in littoral wetlands of urban lake

Wetlands are the largest natural sources of methane (CH4) emissions worldwide. Littoral wetlands of urban lakes represent an ecotone between aquatic and terrestrial ecosystems and are strongly influenced by water levels, environmental conditions, and anthropogenic activities. Despite these littoral zones being potential "hotspots" of CH4 emissions, the status of CH4 emissions therein and the role of physicochemical properties and microbial communities regulating these emissions remain unclear. This study compared the CH4 fluxes, physicochemical properties, and CH4-cycling microbial communities (methanogens and methanotrophs) of three zones (a non-flooded supralittoral zone, a semi-flooded eulittoral zone, and a flooded infralittoral zone) in the littoral wetlands of Lake Pipa, Jiangsu Province, China, for two seasons (summer and winter). The eulittoral zone was a CH4 source (median: 11.49 and 0.02 mg m-2 h-1 in summer and winter, respectively), whereas the supralittoral zone acted as a CH4 sink (median: -0.78 and -0.09 mg m-2 h-1 in summer and winter, respectively). The infralittoral zone shifted from CH4 sink to source between the summer (median: -10.65 mg m-2 h-1) and winter (median: 0.11 mg m-2 h-1). The analysis of the functional genes of methanogenesis (mcrA) and methanotrophy (pmoA) and path analysis showed that CH4 fluxes were strongly regulated by biotic factors (abundance of the mcrA gene and alpha diversity of CH4-cycling microbial communities) and abiotic factors (ammonia nitrogen, moisture, and soil organic carbon). In particular, biotic factors had a major influence on the variation in the CH4 flux, whereas abiotic factors had a minor influence. Our findings provide novel insights into the spatial and seasonal variations in CH4-cycling microbial communities and identify the key factors influencing CH4 fluxes in littoral wetlands. These results are important for managing nutrient inputs and regulating the hydrological regimes of urban lakes.

Experimental erosion of microbial diversity decreases soil CH4 consumption rates

Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4 ) cycle by removing atmospheric CH4 and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution-to-extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 101 -107 -fold, preincubated under a high CH4 atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.

Synthetic phylogenetically diverse communities promote denitrification and stability

Denitrification is an important process of the global nitrogen cycle as some of its intermediates are environmentally important or related to global warming. However, how the phylogenetic diversity of denitrifying communities affects their denitrification rates and temporal stability remains unclear. Here we selected denitrifiers based on their phylogenetic distance to construct two groups of synthetic denitrifying communities: one closely related (CR) group with all strains from the genus Shewanella and the other distantly related (DR) group with all constituents from different genera. All synthetic denitrifying communities (SDCs) were experimentally evolved for 200 generations. The results showed that high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities. Specifically, the productivity and denitrification rates were significantly (P < 0.05) higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community than those in the CR community. The DR community also showed significantly (t = 7.119, df = 10, P < 0.001) higher stability through overyielding and asynchrony of species fluctuations, and showed more complementarity than the CR group during the experimental evolution. This study has important implications for applying synthetic communities to remediate environmental problems and mitigate greenhouse gas emissions.

Synthetic Denitrifying Communities Reveal a Positive and Dynamic Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution

Biodiversity is vital for ecosystem functions and services, and many studies have reported positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships in plant and animal systems. However, if the BEF relationship exists and how it evolves remains elusive in microbial systems. Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) with a richness gradient spanning 1 to 12 species, which were subjected to approximately 180 days (with 60 transfers) of experimental evolution with generational changes in community functions continuously tracked. A significant positive correlation was observed between community richness and functions, represented by productivity (biomass) and denitrification rate, however, such a positive correlation was transient, only significant in earlier days (0 to 60) during the evolution experiment (180 days). Also, we found that community functions generally increased throughout the evolution experiment. Furthermore, microbial community functions with lower richness exhibited greater increases than those with higher richness. Biodiversity effect analysis revealed positive BEF relationships largely attributable to complementary effects, which were more pronounced in communities with lower richness than those with higher richness. This study is one of the first studies that advances our understanding of BEF relationships and their evolutionary mechanisms in microbial systems, highlighting the crucial role of evolution in predicting the BEF relationship in microbial systems. IMPORTANCE Despite the consensus that biodiversity supports ecosystem functioning, not all experimental models of macro-organisms support this notion with positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships reported. The fast-growing, metabolically versatile, and easy manipulation nature of microbial communities allows us to explore well the BEF relationship and further interrogate if the BEF relationship remains constant during long-term community evolution. Here, we constructed multiple synthetic denitrifying communities (SDCs) by randomly selecting species from a candidate pool of 12 Shewanella denitrifiers. These SDCs differ in species richness, spanning 1 to 12 species, and were monitored continuously for community functional shifts during approximately 180-day parallel cultivation. We demonstrated that the BEF relationship was dynamic with initially (day 0 to 60) greater productivity and denitrification among SDCs of higher richness. However, such pattern was reversed thereafter with greater productivity and denitrification increments in lower-richness SDCs, likely due to a greater accumulation of beneficial mutations during the experimental evolution.

NO3- is an important driver of nitrite-dependent anaerobic methane oxidation bacteria and CH4 fluxes in the reservoir riparian zone

Nitrite-dependent anaerobic methane oxidation (N-DAMO) is an important biological process that combines microbial nitrogen and carbon cycling and is mainly carried out by nitrite-dependent anaerobic methane-oxidizing bacteria. The discovery of this microbial process has changed the conventional view of methane oxidation and nitrogen loss. In this study, the abundance, diversity, and community structure of N-DAMO bacteria were investigated based on high-throughput sequencing and fluorescence quantitative PCR measurements. We examined environmental factors driving the variations of CH₄ fluxes and N-DAMO bacterial using correlation analysis and redundancy analysis. We found low CH₄ fluxes and abundant N-DAMO bacteria in the riparian zone. After decomposing the effects of single variables and exploring them, NO₃^- was the only significant factor that significantly correlated with the abundance and richness of the N-DAMO community and gas fluxes (p < 0.05). Under the influence of three different land use types, the increase in NO₃^- (grassland vs. woodland and sparse woods, + 132.81% and + 106.25%) caused structural changes in the composition of the N-DAMO bacterial community, increasing its abundance (- 9.58% and + 21.19%), thus promoting the oxidation of CH₄ and reduced CH₄ emissions (+ 4.78% and + 35.63%) from the riparian zone. Appropriate NO₃^- input helps maintain the existing low methane emission fluxes in the riparian zone of the reservoir.

Pollution alters methanogenic and methanotrophic communities and increases dissolved methane in small ponds

Small ponds have become a hotspot of greenhouse gas emissions, but our understanding of methane (CH₄) cycling and its biological regulation in small polluted ponds remains limited. To assess how pollution affects CH₄ content, we investigated dissolved CH₄ concentrations, water and sediments properties, methanogenic and methanotrophic communities in two types of small polluted ponds. Compared with low pollution (LP) ponds, high pollution (HP) ponds showed significantly (P < 0.05) higher dissolved CH₄ in water. Sequencing of methyl coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) genes showed that HP led to significant (P < 0.05) shifts of CH₄-cycling microbial communities, with increased Shannon index of sediment methanogenic communities and water methanotrophic communities. There were also strong negative associations (P < 0.05) between dissolved CH₄ concentrations and interdomain methanogen-methanotroph network connectivity in water and sediments, respectively. The partial least squares path modeling indicated that dissolved oxygen, total organic carbon, ammonium nitrogen and nitrate nitrogen of water, and total nitrogen and total carbon of sediment, and CH₄-cycling microbes could regulate the CH₄ content. This study clarified the effects of environmental deterioration on CH₄ cycling in small ponds, highlighting the use of methanogen-methanotroph network connectivity to assess the CH₄ production.

Nitrogen addition decreases methane uptake caused by methanotroph and methanogen imbalances in a Moso bamboo forest

Forest soils play an important role in controlling global warming by reducing atmospheric methane (CH₄) concentrations. However, little attention has been paid to how nitrogen (N) deposition may alter microorganism communities that are related to the CH₄ cycle or CH₄ oxidation in subtropical forest soils. We investigated the effects of N addition (0, 30, 60, or 90 kg N ha⁻¹ yr⁻¹) on soil CH₄ flux and methanotroph and methanogen abundance, diversity, and community structure in a Moso bamboo (Phyllostachys edulis) forest in subtropical China. N addition significantly increased methanogen abundance but reduced both methanotroph and methanogen diversity. Methanotroph and methanogen community structures under the N deposition treatments were significantly different from those of the control. In N deposition treatments, the relative abundance of Methanoculleus was significantly lower than that in the control. Soil pH was the key factor regulating the changes in methanotroph and methanogen diversity and community structure. The CH₄ emission rate increased with N addition and was negatively correlated with both methanotroph and methanogen diversity but positively correlated with methanogen abundance. Overall, our results suggested that N deposition can suppress CH₄ uptake by altering methanotroph and methanogen abundance, diversity, and community structure in subtropical Moso bamboo forest soils.

Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function

Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH₄ )-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH₄ oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.

Community-level signatures of ecological succession in natural bacterial communities

A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We profiled (16S rRNA sequencing)  > 700 semi-aquatic bacterial communities while measuring their functional capacity when grown in laboratory conditions. This approach allowed us to investigate the relationship between composition and function excluding confounding environmental factors. Simulated data allowed us to reject the hypothesis that stochastic processes were responsible for community assembly, suggesting that niche effects prevailed. Consistent with this idea we identified six distinct community classes that contained samples collected from distant locations. Structural equation models showed there was a functional signature associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions (PiCRUST). This approach allowed us to show that the classes contained distinct genetic repertoires reflecting community-level ecological strategies. The ecological strategies resemble the classical distinction between r- and K-strategists, suggesting that bacterial community assembly may be explained by simple ecological mechanisms.

Linking microbial communities to ecosystem functions: what we can learn from genotype-phenotype mapping in organisms

Microbial physiological processes are intimately involved in nutrient cycling. However, it remains unclear to what extent microbial diversity or community composition is important for determining the rates of ecosystem-scale functions. There are many examples of positive correlations between microbial diversity and ecosystem function, but how microbial communities 'map' onto ecosystem functions remain unresolved. This uncertainty limits our ability to predict and manage crucial microbially mediated processes such as nutrient losses and greenhouse gas emissions. To overcome this challenge, we propose integrating traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping in organisms. We identify two insights from genotype-phenotype mapping that could be useful for microbial biodiversity-ecosystem function studies: the concept of searching 'agnostically' for markers of ecosystem function and controlling for population stratification to identify microorganisms uniquely associated with ecosystem function. We illustrate the potential for these approaches to elucidate microbial biodiversity-ecosystem function relationships by analysing a subset of published data measuring methane oxidation rates from tropical soils. We assert that combining the approaches of traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping will generate novel hypotheses about how complex microbial communities drive ecosystem function and help scientists predict and manage changes to ecosystem functions resulting from human activities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Metabolically cohesive microbial consortia and ecosystem functioning

Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in the context of competition for resources and metabolic complementarity given that, in microbial communities (MCs), many excreted by-products of metabolism may also be resources. MCs therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organization between the species and the community level may be pervasive, where tightly knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community- and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.