Rrn Copy Number Research Articles

Microbial rrn copy number is associated with soil C: N ratio and pH under long-term fertilization

Soil microbial life-history strategies, as indicated by rRNA operon (rrn) copy numbers, strongly influence agro-ecosystem functioning. Long-term N fertilization causes strong and lasting changes in soil properties, yet its impact on microbial strategies remains largely unexplored. Using long-term field experiments across three agro-ecosystems, we consistently found that N fertilization strongly decreased soil C: N ratio and pH, further increasing the community-level rrn copy number, including both average rrn copy number and total 16S rRNA copy number. Soil C: N stoichiometry balanced by N supplement favored the growth of N-dependent copiotrophic species containing high rrn copy numbers (an average of 2.5) and increased their network connections, predominantly contributing to community-level rrn copy number increase. Decreased soil pH caused by N fertilization also favored the growth of some species whose abundances negatively correlated with pH, partially contributing to the community-level rrn copy number increase. By examining the genomes of two dominant species, we found that microorganisms with a higher rrn copy number (6), e.g., Streptomyces scabiei, possessed more genes related to C and N transport and metabolism. In contrast, the Mycobacterium simiae with a lower rrn copy number (1) has more genes associated with secondary metabolite biosynthesis and lipid transport and metabolism. Our finding challenges the concept of microbial life-strategy regulation solely by nutrient availability, highlighting the important contributions of soil stoichiometric balance and pH to microbial strategies in agro-ecosystems under long-term N inputs.

Recovery of bacterial network complexity and stability after simulated extreme rainfall is mediated by K−/r-strategy dominance

The complexity and stability of belowground microbial communities are among the core mechanisms that drive ecosystem functions. Disturbances, such as climate extremes, can exert a substantial influence on these microbial attributes. However, the role of the microbial life history strategy in determining the complexity and stability of desert soil microbial communities after extreme rainfall is poorly understood. Here, we explored the response patterns of bacterial network complexity and stability and characterized the bacterial life history strategy on the basis of the oligotroph (K-strategist)-to-copiotroph (r-strategist) ratio after three extreme rainfall treatments (11, 15, and 25 mm). Experimental results demonstrated that the bacterial communities immediately shifted from the K-strategy to the r-strategy one day after extreme rainfall and gradually recovered to the K-strategy over time, as verified by the increase (31.46 %–125.51 %) then decrease (41.51 % – 95.78 %) in the weighted rrn copy number. Meanwhile, bacterial network complexity and stability showed three-phase patterns [dramatic decline (decreased by 211.67 %–388.46 %)–gradual recovery (increased by 45.60 %–103.65 %)–insignificant change] after three extreme rainfall events. The decline/recovery of these bacterial attributes was highly pronounced/slow after the large extreme rainfall treatment. Specifically, the responses of bacterial network complexity and stability to extreme rainfall showed negative correlations with the response of the weighted rrn copy number (R = -0.55 – -0.74, P < 0.01). The mechanisms underlying the response patterns of bacterial network complexity and stability were related to the prevalence of the r-strategy of the bacterial communities (Phase 1) and the shifts from the r-strategy to the K-strategy due to the gradual reduction in soil moisture (Phase 2 and 3). These results emphasize the importance of the microbial life history strategy in maintaining network complexity and stability and help in understanding how belowground communities can withstand future disturbances.

Long-term nitrogen input reduces soil bacterial network complexity by shifts in life history strategy in temperate grassland.

We investigated soil bacterial and fungal communities, constructed co-occurrence networks, and estimated bacterial traits along a gradient of nitrogen (N) input. The results showed that soil bacterial co-occurrence networks complexity decreased with increasing N input. The ratio of negative to positive cohesion decreased with increasing N input, suggesting the declined competitive but strengthened cooperative interactions. However, soil fungal network complexity did not change under N enrichment. In addition, N input stimulated the copiotroph/oligotroph ratio, ribosomal RNA operon (rrn) copy number, and guanine-cytosine (GC) content of soil bacteria, shifting bacterial life history strategy toward copiotroph with increased r-/K-strategy ratio. Piecewise structural equation modeling results further revealed that the reduction in bacterial co-occurrence network complexity was directly regulated by the increased bacterial r-/K-strategy ratio, rather than reduced bacterial richness. Our study reveals the mechanisms through which microbial traits regulate interactions and shape co-occurrence networks under global changes.

Oligotrophic microbes are recruited to resist multiple global change factors in agricultural subsoils

An increasing number of anthropogenic pressures can have negative effects on biodiversity and ecosystem functioning. However, our understanding of how soil microbial communities and functions in response to multiple global change factors (GCFs) is still incomplete, particularly in less frequently disturbed subsoils. In this study, we examined the impact of different levels of GCFs (0–9) on soil functions and bacterial communities in both topsoils (0–20 cm) and subsoils (20–40 cm) of an agricultural ecosystem, and characterized the intrinsic factors influencing community resistance based on microbial life history strategy. Our experimental results showed a decline in soil multifunctionality, bacterial diversity, and community resistance as the number of GCFs increased, with a more drastic reduction in community resistance of subsoils. Specifically, we observed a significantly positive relationship between the oligotroph/copiotroph ratio and community resistance in subsoils, which was also verified by the negative correlation between 16S rRNA operon (rrn) copy number and community resistance. Structural equation modeling further revealed the direct effects of community resistance in promoting the ecosystem functioning, regardless of top- and subsoils. Therefore, these results suggested that subsoils may recruit more oligotrophic microbes to enhance their originally weaker community resistance under multiple GCFs, which was essential for maintaining sustainable agroecological functions and services. Overall, our study represents a significant advance in linking microbial life history strategy to the resistance of belowground microbial community and functionality.

Accelerated organic matter decomposition in thermokarst lakes upon carbon and phosphorus inputs.

Mineralization of dissolved organic matter (DOM) in thermokarst lakes plays a non-negligible role in the permafrost carbon (C) cycle, but remains poorly understood due to its complex interactions with external C and nutrient inputs (i.e., aquatic priming and nutrient effects). Based on large-scale lake sampling and laboratory incubations, in combination with 13 C-stable-isotope labeling, optical spectroscopy, and high-throughput sequencing, we examined large-scale patterns and dominant drivers of priming and nutrient effects of DOM biodegradation across 30 thermokarst lakes along a 1100-km transect on the Tibetan Plateau. We observed that labile C and phosphorus (P) rather than nitrogen (N) inputs stimulated DOM biodegradation, with the priming and P effects being 172% and 451% over unamended control, respectively. We also detected significant interactive effects of labile C and nutrient supply on DOM biodegradation, with the combined labile C and nutrient additions inducing stronger microbial mineralization than C or nutrient treatment alone, illustrating that microbial activity in alpine thermokarst lakes is co-limited by both C and nutrients. We further found that the aquatic priming was mainly driven by DOM quality, with the priming intensity increasing with DOM recalcitrance, reflecting the limitation of external C as energy sources for microbial activity. Greater priming intensity was also associated with higher community-level ribosomal RNA gene operon (rrn) copy number and bacterial diversity as well as increased background soluble reactive P concentration. In contrast, the P effect decreased with DOM recalcitrance as well as with background soluble reactive P and ammonium concentrations, revealing the declining importance of P availability in mediating DOM biodegradation with enhanced C limitation but reduced nutrient limitation. Overall, the stimulation of external C and P inputs on DOM biodegradation in thermokarst lakes would amplify C-climate feedback in this alpine permafrost region.

Ribosomal RNA gene operon copy number, a functional trait indicating the hydrocarbon degradation level of bacterial communities

The lack of universal indicators for predicting microbial biodegradation potential and assessing remediation effects limits the generalization of bioremediation. The community-level ribosomal RNA gene operon (rrn) copy number, an important functional trait, has the potential to serve as a key indicator of the bioremediation of organic pollutants. A meta-analysis based on 1275 samples from 26 hydrocarbon-related studies revealed a positive relationship between the microbial hydrocarbon biodegradation level and the community-level rrn copy number in soil, seawater and culture. Subsequently, a microcosm experiment was performed to decipher the community-level rrn copy number response mechanism during total petroleum hydrocarbon (TPH) biodegradation. The treatment combining straw with resuscitation-promoting factor (Rpf) exhibited the highest community-level rrn copy number and the most effective biodegradation compared with other treatments, and the initial TPH content (20,000 mg kg-1) was reduced by 67.67% after 77 days of incubation. TPH biodegradation rate was positively correlated with the average community-level rrn copy number (p = 0.001, R2 = 0.5781). Both meta and community analyses showed that rrn copy number may reflect the potential of hydrocarbon degradation and microbial dormancy. Our findings provide insight into the applicability of the community-level rrn copy number to assess bacterial biodegradation for pollution remediation.

Microbes drive metabolism, community diversity, and interactions in response to microplastic-induced nutrient imbalance

The impact of conventional and biodegradable microplastics on soil nutrients (carbon and nitrogen) has been widely examined, and the alteration of nutrient conditions further influences microbial biosynthesis processes. Nonetheless, the influence of microplastic-induced nutrient imbalances on soil microorganisms (from metabolism to community interactions) is still not well understood. We hypothesized that conventional and biodegradable microplastic could alter soil nutrients and microbial processes. To fill this knowledge gap, we conducted soil microcosms with polyethylene (PE, new and aged) and polylactic acid (PLA, new and aged) microplastics to evaluate their effects on the soil enzymatic stoichiometry, co-occurrence interactions, and success patterns of soil bacterial communities. New and aged PLA induced soil N immobilization, which decreased soil mineral N by 91–141 %. The biodegradation of PLA led to a higher bioavailable C and wider bioavailable C:N ratio, which further filtered out specific microbial species. Both new and aged PLA had a higher abundance of copiotrophic members (Proteobacteria, 35–51 % in PLA, 26–34 % in CK/PE treatments) and rrn copy number. The addition of PLA resulted in a lower alpha diversity and reduced network complexity. Conversely, because of the chemically stable hydrocarbon structure of PE polymers, the new and aged PE microplastics had a minor effect on soil mineral N, bacterial community composition, and network complexity, but led to microbial C limitation. Collectively, all microplastics increased soil C-, N-, and P -acquiring enzyme activities and reduced the number of keystone species and the robustness of the co-occurrence network. The PLA treatment enhanced nitrogen fixation and ureolysis, whereas the PE treatment increased the degradation of recalcitrant carbon. Overall, the alteration of soil nutrient conditions by microplastics affected the microbial metabolism and community interactions, although the effects of PE and PLA microplastics were distinct.

Trade-off between microbial ecophysiological features regulated by soil fertility governs plant residue decomposition

Soil fertility influences microbial-driven plant residue decomposition, thus further affecting soil organic carbon (C) formation. Both ecological and physiological features of microbial communities change with soil fertilities, however, the mechanism of how soil fertility influences microbial ecophysiological features (both the taxonomic and functional profiles) driving plant residue decomposition is unclear. Here, four series of microcosms were set up, inoculated with two distinct soils, each with low and high fertility levels as a result of contrasting long-term fertilization regimes, and incubated with 13C-labeled rice straw amendments. DNA stable-isotope probing (DNA-SIP) based amplicon sequencing and shotgun metagenomic sequencing were conducted. We found that both bacterial community composition (including the relative abundance, α- and β-diversities, and taxonomic composition) and carbohydrate metabolic efficiency were significantly changed under different soil fertilities. High fertile soils gave rise to greater increases in bacterial populations and straw decomposition than low fertile soils, yet DNA-SIP-based shotgun metagenomic sequencing showed that the bacterial average carbohydrate metabolic efficiency, characterized by the average carbohydrate-active enzyme (CAZyme) abundance within each bacterial phylum was significantly lower. Linear regressions between bacterial ribosomal RNA operon (rrn) copy number and bacterial carbohydrate metabolic efficiency under contrasting soil fertilities suggested that high fertile soils select for fast-but-inefficient bacteria to degrade rice straw while low fertile soils select for slow-but-efficient ones. Collectively, the data demonstrate a fundamental trade-off between the ecological and physiological attributes of straw-degrading microbial communities. The trade-off is regulated by soil fertility and in turn governs plant residue decomposition. This work provides novel insights for better understanding the ecological and physiological roles of microbes in organic matter decomposition and global terrestrial C cycling, especially in the context of crop straw degradation under contrasting soil fertilities.

Community rRNA operon copy number of soil bacteria decreases with soil depth and ecosystem succession in postglacial ecosystems

rRNA operon (rrn) copy number is a functional trait that reflects the ecological strategies of bacteria. Here, we estimated the average rrn copy number of soil bacterial communities in postglacial ecosystems of Mount Gongga using the 16S rRNA gene sequencing data and the ancestral trait reconstruction method. We found that the community rrn copy number decreased with soil depth and ecosystem succession. More than 90 % of the variations were explained by soil pH and resource availability, indicating that this trait was under strong selection pressure of environmental factors. Thus, community rrn copy number may reveal the changes in bacterial community from the perspective of adaptive strategies, which is a complement to the taxonomic approach.

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Soil microbiomes are sensitive to current and previous soil conditions, and bacterial ‘bioindicators’ of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

Microbial life strategy with high rRNA operon copy number facilitates the energy and nutrient flux in anaerobic digestion

Microbial life strategy, reflected by rRNA operon (rrn) copy number, determines microbial ecological roles. However, the relationship between microbial life strategy and the energy and nutrient flux in anaerobic digestion (AD) remains elusive. This study investigated microbial rrn copy number and expression ratio using amplicon sequencing of 16S rRNA gene and 16S rRNA, and monitored CH4 daily production to approximate the status of energy and nutrient flux in semi-continuous AD. A significantly positive correlation between the mean rrn copy number of microbial communities in digestate and CH4 daily production was detected in the control treatment fed swine manure. The reduced feedstock complexity, by replacing parts of swine manure with fructose or apple waste, weakened the correlation. When feedstock complexity was increased again, the correlation was strengthened again. Similar results were detected in mean rrn expression ratio of microbial communities. The responses of mean rrn copy number and expression ratio of communities to feedstock addition differed between the reduced feedstock complexity and the control treatment, as well as between in digestate and in straw. Our findings reveal a novel relationship between microbial community life strategy and the energy and nutrient flux, and the roles of feedstock characteristics therein in AD.

Manure application effects on subsoils: Abundant taxa initiate the diversity reduction of rare bacteria and community functional alterations

Manure application is a significant agriculture practice that can affect the microbial community structure in both topsoil and subsoil. However, how the abundant and rare taxa in the soil profile respond to surface manure application and their ecological roles at different soil depths remain unknown. Based on a soil mesocosm experiment, we used amplicon sequencing and high-throughput quantitative-PCR array to characterize the bacterial community composition and functional traits across soil profiles. Results showed that the relative abundance and diversity of rare taxa increased in the topsoil but decreased in the 40–60 cm soil, where the relative abundance of abundant taxa increased after manure application. Evidence from network analysis, niche width and 16S rRNA operon (rrn) copy number suggest that abundant taxa in subsoils had a greater competitivity for resource mining than rare taxa. Regarding resource utilization strategies, microbial communities under manure treatment preferred to utilize recalcitrant carbon (C) and inorganic phosphorus (P) in the topsoil and labile carbon and organic phosphorus in the subsoil compared with non-manure application. Random Forest regression analysis indicated the relatively greater contribution of abundant taxa to C degradation and fixation in subsoils. These results imply that the manure application effect on microbial resource mining in subsoils is mainly driven by abundant bacteria due to the lower competitiveness of rare taxa for the C sources leached above. Overall, This study linked community functions with the ecological role of abundant and rare taxa in the context of environmental disturbances at different soil depths and shed light on the potential ecological risks of diversity reduction of subsoil rare bacteria.

Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies.

Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, we characterized the genomic traits, exometabolite profiles, and interactions of soil bacteria representing copiotrophic and oligotrophic strategists. Isolates were selected based on differences in ribosomal RNA operon (rrn) copy number, as a proxy for life-history strategies, with pairs of “high” and “low” rrn copy number isolates represented within the Micrococcales, Corynebacteriales, and Bacillales. We found that high rrn isolates consumed a greater diversity and amount of substrates than low rrn isolates in a defined growth medium containing common soil metabolites. We estimated overlap in substrate utilization profiles to predict the potential for resource competition and found that high rrn isolates tended to have a greater potential for competitive interactions. The predicted interactions positively correlated with the measured interactions that were dominated by negative interactions as determined through sequential growth experiments. This suggests that resource competition was a major force governing interactions among isolates, while cross-feeding of metabolic secretion likely contributed to the relatively rare positive interactions observed. By connecting bacterial life-history strategies, genomic features, and metabolism, our study advances the understanding of the links between bacterial community composition and the transformation of carbon in soils.

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

Evaluating the Potential Antibiotic Resistance Status in Environment Based on the Trait of Microbial Community.

The overuse of antibiotics has promoted the propagation and dissemination of antibiotic resistance genes (ARGs) in environment. Due to the dense human population and intensive activities in coastal areas, the health risk of ARGs in coastal environment is becoming a severe problem. To date, there still lacks of a quantitative method to assess properly the gross antibiotic resistance at microbial community level. Here, we collected sediment samples from Hangzhou Bay (HB), Taizhou Bay (TB), and Xiangshan Bay (XB) of the East China Sea for community-level ARGs analysis. Based on the 16S rRNA genes and predictive metagenomics, we predicted the composition of intrinsic ARGs (piARGs) and some related functional groups. Firstly, a total of 40 piARG subtypes, belonging to nine drug classes and five resistance mechanisms, were obtained, among which the piARGs encoding multidrug efflux pumps were the most dominant in the three bays. Secondly, XB had higher relative abundances of piARGs and pathogens than the other two bays, which posed higher potential health risk and implied the heavier impact of long-term maricultural activities in this bay. Thirdly, the co-occurrence network analysis identified that there were more connections between piARGs and some potential pathogenic bacteria. Several piARG subtypes (e.g., tetA, aacA, aacC, and aadK) distributed widely in the microbial communities. And finally, the microbial diversity correlated negatively with the relative abundance of piARGs. Oil, salinity, and arsenic had significant effects on the variations of piARGs and potential pathogenic bacteria. The abundance-weighted average ribosomal RNA operon (rrn) copy number of microbial communities could be regarded as an indicator to evaluate the antibiotic resistance status. In conclusion, this study provides a new insight on how to evaluate antibiotic resistance status and their potential risk in environment based on a quantitative analysis of microbial communities.

Dynamics of coastal bacterial community average ribosomal RNA operon copy number reflect its response and sensitivity to ammonium and phosphate

The nutrient-rich effluent from wastewater treatment plants (WWTPs) constitutes a significant disturbance to coastal microbial communities, which in turn affect ecosystem functioning. However, little is known about how such disturbance could affect the community’s stability, an important knowledge gap for predicting community response to future disturbances. Here, we examined dynamics of coastal sediment microbial communities with and without a history of WWTP’s disturbances (named H1 and H0 hereafter) after simulated nutrient input loading at the low level (5 mg L−1 NH4+-N and 0.5 mg L−1 PO43--P) or high level (50 mg L−1 NH4+-N and 5.0 mg L−1 PO43--P) for 28 days. H0 community was highly sensitive to both low and high nutrient loading, showing a faster community turnover than H1 community. In contrast, H1 community was more efficient in nutrient removal. To explain it, we found that H1 community constituted more abundant and diversified r-strategists, known to be copiotrophic and fast in growth and reproduction, than H0 community. As nutrient was gradually consumed, both communities showed a succession of decreasing r-strategists. Accordingly, there was a decrease in community average ribosomal RNA operon (rrn) copy number, a recently established functional trait of r-strategists. Remarkably, the average rrn copy number of H0 communities was strongly correlated with NH4+-N (R2 = 0.515, P = 0.009 for low nutrient loading; R2 = 0.749, P = 0.001 for high nutrient loading) and PO43--P (R2 = 0.378, P = 0.034 for low nutrient loading; R2 = 0.772, P = 0.001 for high nutrient loading) concentrations, while that of H1 communities was only correlated with NH4+-N at high nutrient loading (R2 = 0.864, P = 0.001). Our results reveal the potential of using rrn copy number to evaluate the community sensitivity to nutrient disturbances, but community’s historical contingency need to be taken in account.

Wastewater microbial community structure and functional traits change over short timescales

Wastewater contains microorganisms coming from various sources, e.g. feces discharges, soil infiltrations and sewer biofilms and sediments. The primary objective of this work was to determine if end-of-pipe wastewater microbial community structures exhibits short-timescale variation, and assess possible microbial origins. To this end, we measured hourly physicochemical characteristics of wastewater influent for 2 days and analyzed the microbial community at 4-h intervals using 16S rRNA gene amplicon sequencing. Results showed large variations in the microbial community composition at phylum and genus levels, i.e. Proteobacteria ranged from 44 to 63% of the total relative abundance and Arcobacter ranged from 11 to 22%. Diurnal patterns were observed in the alpha-diversity, beta-diversity and the prevalence of several taxa. Wastewater physicochemical characteristics explained 61% of the total microbial community variance by Canonical Correspondence Analysis (CCA), with flow rate being the main explanatory variable exhibiting a clear diurnal profile. Comparison with public databases using closed reference OTUs revealed that only 7.3% of the sequences were shared with human gut microbiota and 21.7% with soil microbiota, the majority being from the sewer biofilms and sediments. The functional trait, weighted average ribosomal RNA operon (rrn) copy number per genome, was found to be relatively high in the wastewater microbiota (average 3.6, soil 2.1, and human gut 2.6) and significantly correlated with flow, inferring active microbial enrichments in the sewer. The prevalence of Methylophilaceae, methanol oxidation genes and denitrification genes were related to high influent methanol and NO3− concentration in the influent wastewater. These functional organisms and genes indicate important carbon and nutrient removal related functions in the sewer. Together, the observed temporal patterns of the microbial community and functional traits suggest that high wastewater flow causes greater transport of active sewer microorganisms which are functionally important.

Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials

The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3−) (−27.4%) and ammonium (NH4+) (−15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.

Ecological strategies and metabolic trade-offs of complex environmental biofilms

Microorganisms aggregated into matrix-enclosed biofilms dominate microbial life in most natural, engineered, and medical systems. Despite this, the ecological adaptations and metabolic trade-offs of the formation of complex biofilms are currently poorly understood. Here, exploring the dynamics of bacterial ribosomal RNA operon (rrn) copy numbers, we unravel the genomic underpinning of the formation and success of stream biofilms that contain hundreds of bacterial taxa. Experimenting with stream biofilms, we found that nascent biofilms in eutrophic systems had reduced lag phases and higher growth rates, and more taxa with higher rrn copy number than biofilms from oligotrophic systems. Based on these growth-related traits, our findings suggest that biofilm succession was dominated by slow-but-efficient bacteria likely with leaky functions, such as the production of extracellular polymeric substances at the cost of rapid growth. Expanding our experimental findings to biofilms from 140 streams, we found that rrn copy number distribution reflects functional trait allocation and ecological strategies of biofilms to be able to thrive in fluctuating environments. These findings suggest that alternative trade-offs dominating over rate-yield trade-offs contribute to the evolutionary success of stream biofilms.

The unconstrained evolution of fast and efficient antibiotic-resistant bacterial genomes.

Evolutionary trajectories are constrained by trade-offs when mutations that benefit one life history trait incur fitness costs in other traits. As resistance to tetracycline antibiotics by increased efflux can be associated with an increase in length of the Escherichia coli chromosome of 10% or more, we sought costs of resistance associated with doxycycline. However, it was difficult to identify any because the growth rate (r), carrying capacity (K) and drug efflux rate of E. coli increased during evolutionary experiments where the species was exposed to doxycycline. Moreover, these improvements remained following drug withdrawal. We sought mechanisms for this seemingly unconstrained adaptation, particularly as these traits ought to trade-off according to rK selection theory. Using prokaryote and eukaryote microorganisms, including clinical pathogens, we show that r and K can trade-off, but need not, because of 'rK trade-ups'. r and K trade-off only in sufficiently carbon-rich environments where growth is inefficient. We then used E. coli ribosomal RNA (rRNA) knockouts to determine specific mutations, namely changes in rRNA operon (rrn) copy number, than can simultaneously maximize r and K. The optimal genome has fewer operons, and therefore fewer functional ribosomes, than the ancestral strain. It is, therefore, unsurprising for r-adaptation in the presence of a ribosome-inhibiting antibiotic, doxycycline, to also increase population size. We found two costs for this improvement: an elongated lag phase and the loss of stress protection genes.