Full Open Population Capture–Recapture Models With Individual Covariates

Traditional analyses of capture–recapture data are based on likelihood functions that explicitly integrate out all missing data. We use a complete data likelihood (CDL) to show how a wide range of capture–recapture models can be easily fitted using readily available software JAGS/BUGS even when there are individual-specific time-varying covariates. The models we describe extend those that condition on first capture to include abundance parameters, or parameters related to abundance, such as population size, birth rates or lifetime. The use of a CDL means that any missing data, including uncertain individual covariates, can be included in models without the need for customized likelihood functions. This approach also facilitates modeling processes of demographic interest rather than the complexities caused by non-ignorable missing data. We illustrate using two examples, (i) open population modeling in the presence of a censored time-varying individual covariate in a full robust design, and (ii) full open population multi-state modeling in the presence of a partially observed categorical variable. Supplemental materials for this article are available online.     

Climate change is linked to long-term decline in a stream salamander

Amphibian declines have been documented worldwide and several have been linked to climate change, but the long-term data needed to detect declines are largely restricted to pond-breeding species. This limits our knowledge of population trends in other major groups of amphibians, including stream salamanders, which have their greatest diversity in North America. I hypothesized that increasing air temperature and precipitation in northeastern North America caused abundance of the stream salamander Gyrinophilus porphyriticus in a New Hampshire population to decline between 1999 and 2010. I found a significant decline in abundance of G. porphyriticus adults over this 12-year period, and no trend in larval abundance. Adult abundance was negatively related to annual precipitation, which is predicted to increase further in the Northeast due to climate change. Analysis of a 6-year capture–mark–recapture data set for the same population showed no temporal variation in larval and adult detectability, validating the abundance data, and no variation in larval and adult survival. However, survival during metamorphosis from the larval to adult stage declined dramatically. These results suggest that increasing precipitation is causing a decline in adult recruitment, which, if it persists, will lead to local extinction. A likely mechanism for the decline in adult recruitment is mortality of metamorphosing individuals during spring and fall floods, which have increased in volume and frequency with the increase in precipitation. More broadly, this study presents strong evidence that the amphibian decline crisis extends to North America’s stream salamanders, and shows the critical need to collect population data on these species.     

Confidence intervals for expected abundance of rare species

In many ecological research studies, abundance data are skewed and contain more zeros than might be expected. Often, the aim is to model abundance in terms of covariates, and to estimate expected abundance for a given set of covariate values. An approach that has been advocated recently involves the use of a conditional model. This allows one to separately model presence and abundance given presence, which should lead to a more complete understanding as to how the covariates influence abundance. The focus of this article is on the calculation of confidence intervals for expected abundance given particular values of the covariates. The standard Wald confidence interval is symmetric, and therefore unlikely to be of much use for skewed data, where reliable confidence intervals for abundance will generally be asymmetric. The purpose of this article is to show how to calculate a profile likelihood confidence interval for expected abundance using a conditional model.     

Response of archaeal communities to water regimes under simulated warming and drought conditions in Tibetan Plateau wetlands

Purpose

Understanding how archaeal communities are affected by water-table drawdown is essential for predicting soil functional responses to future climate change and the consequences of the responses on the soil carbon cycle.

Material and methods

We investigated the effect of water-table drawdown, warming, drought, and combinations thereof on archaeal communities using terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR.

Results and discussion

Methanosarcinales, Methanosaeta, Methanomicrobiales, Methanobacteriales, uncultured Rice Cluster II (RC-II), and uncultured Crenarchaeota were detected. Water-table drawdown and drought exhibited significant effects on the archaeal communities. When the water table was at or above 10 cm, the archaeal abundance at 10 cm remained high (approximately 10⁹ cells per gram dry soil), whereas the archaeal abundance at 10 cm was reduced to approximately 10⁸ cells per gram dry soil where the water table was lowered to 20 cm or below. When the water table kept constant, warming caused a significant reduction in the archaeal abundance, whereas drought only caused a decrease in archaeal abundance when the water table was higher than ?20 cm.

Conclusions

Results suggest that changes in water table may directly impact archaeal community abundance and assemblage which can in turn influence methane emissions, potentially on a large scale. Our results also indicate that archaeal communities response to water-table drawdowns that are dependent on the initial ecohydrology.

     

Assessing sensitivity to climate change and drought variability of a sand dune endemic lizard

Bioclimatic models aimed assessing a species’ sensitivity to climate change incorporate mean shifts in climate variables; however the more acute threat to the persistence of species may result from increased frequency of extreme climatic events, including increased duration and severity of droughts. Here we assess climate-change sensitivity using niche modeling that unlike bioclimatic modeling incorporates both climate variables as well as other habitat features that constrain a species’ distribution. We analyzed the effects of potential increases in drought frequency for an endangered, sand dune-restricted lizard, a species restricted to a narrowly occurring substrate and so unable to move up-slope or pole-ward to track climate shifts. Our niche modeling results indicated only minor losses to the area of suitable niche space at lower levels of modeled climate change; at the most severe climate shifts we tested the area of suitable niche space reduced by slightly more than 50%. However, extrapolating the potential impacts of reduced rainfall on drought periodicity and intensity showed a more immediate and acute impact on the lizard’s populations. Drought duration projections coupled with landscape fragmentation resulted in rapid losses of suitable niche space, beginning in the more arid portion of the lizard’s range and extending into more moderate climate areas. Although there is greater uncertainty associated with the impacts of climate change on drought periodicity than with shifts in mean conditions, our results show a greater potential for droughts to negatively impact species’ resilience to such changes.     

The short-term effects of nitrification inhibitors on the abundance and expression of ammonia and nitrite oxidizers in a long-term field experiment comparing land management

Microcosms were set up to evaluate the effect of nitrification inhibitors (DCD, c-PTiO, and NaClO₃) on the abundance and expression of ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as the nitrite-oxidizing bacteria (NOB) Nitrospira and Nitrobacter. Both DCD and NaClO₃ inhibited the net nitrification rate, while c-PTiO had no significant effects, and NaClO₃ had a much greater inhibitory effect (> 60%) in all soils than DCD. No significant changes in total microbial abundance were observed with DCD and NaClO₃. DCD limited only the growth of AOB; however, NaClO₃ inhibited growth of both AOA and Nitrospira-NOB with no significant effects on AOB and Nitrobacter-NOB. Probably NaClO₃ inhibited both ammonia oxidation and nitrite oxidation. This is the first report to reveal the inhibitory effects of NaClO₃ on a specific nitrification process, helping to clarify the ecological niche of nitrifiers and the potential of nitrification inhibitors applied to soil.     

Identification of resistance to <Emphasis Type="Italic">Bemisia tabaci</Emphasis> Genn. in closely related wild relatives of cultivated tomato based on trichome type analysis and choice and no-choice assays

The sweetpotato whitefly, Bemisia tabaci Genn., is a major pest of tomato (Solanum lycopersicum) and other crops throughout the tropics and subtropics. The objectives of this study were to characterize 255 accessions of S. galapagense, S. cheesmaniae and S. pimpinellifolium for trichome types, and to evaluate selected accessions with high densities of glandular trichomes for resistance to whitefly. Twenty-two accessions classified as either sparse or abundant for type IV trichomes were selected and evaluated for numbers of adults, eggs, nymphs, and puparium of whitefly in choice bioassays, for adult mortality and egg numbers in no-choice bioassays, and for densities of type I, IV, V, and VI trichomes. The highest whitefly resistance was detected in S. galapagense accessions VI063177 and VI037239 based on choice and no-choice bioassays. In addition, we found high levels of whitefly resistance in S. cheesmaniae accession VI037240 based on the choice bioassay and in S. pimpinellifolium accession VI030462 based on the no-choice bioassay. Whitefly resistance in VI037240 and VI030462 is noteworthy because these species are closely related to cultivated tomato and introgression of whitefly resistance should be relatively straightforward. High densities of type IV trichomes and low densities of type V trichomes were associated with reduced numbers of whitefly adults, nymphs, puparium, and eggs in the choice bioassay and with high adult whitefly mortality in the no-choice bioassay. Preliminary trichome analysis followed by choice and no-choice assays facilitated rapid identification of whitefly-resistant accessions from a large pool of candidates of different species.     

Relationship between spike morphology and habitat of four <Emphasis Type="Italic">Aegilops</Emphasis> species of section Sitopsis

This study examines the relationship between spike morphology and natural habitat for 84 accessions of four Aegilops species, belongs to section Sitopsis, Ae. bicornis, Ae. longissima, Ae. searsii, and Ae. sharonensis in genus Aegilops, section Sitopsis, wild relatives of Triticum aestivum L. These species are considered valuable genetic resources for future cultivation and breeding of domesticated wheat. The goals of the study were to: (1) document variation in spike morphology among these four species; (2) examine the relationship between spike morphology and native habitat; (3) document geographical distribution of distinct spike morphology; and (4) examine the relationship between spike morphology and heading time and value for these four species. The results reveal significant differences in spike morphology among species of section Sitopsis. The most noteworthy variation involved the absence/presence of lateral awn, such that species with lateral awn were restricted in coastal, though species without lateral awn were mainly distributed in inland. This suggests that local climate may be a determinant of variation in lateral awn, and that this trait may be subject to convergent evolution. Differences in heading time in sympatric area were also observed. The differences may enhance species divergence and could represent a lead speciation event. The results of this study will facilitate identification of populations or accessions of wild wheat with favorable traits and/or novel adaptive genes.     

Geographic distance and amorphous iron affect the abundance and distribution of <Emphasis Type="Italic">Geobacteraceae</Emphasis> in paddy soils in China

Purpose

Geobacteraceae are important dissimilatory Fe (III)-reducing microorganisms, influencing the cycling of metals, nutrients as well as the degradation of organic contaminants. However, little is known about their distribution, diversity, and abundance of Geobacteraceae and the effects of environment factors and geographic distance on the distribution and diversity of Geobacteraceae in paddy soils remain unclear. Therefore, the objectives of this study were to investigate the distribution, diversity, and abundance of Geobacteraceae in paddy soils and to determine key factors in shaping the Geobacteraceae distribution, environmental factors, geographic distance, or both and to quantify their contribution to Geobacteraceae variation.

Materials and methods

Illumina sequencing and quantitative real-time PCR using a primer set targeting 16S rRNA genes of bacteria affiliated with the family Geobacteraceae were employed to measure the community composition, diversity, and abundance patterns of 16S rRNA genes of Geobacteraceae in 16 samples collected from north to south of China. MRT, Mantel test, and VPA were used to analyze the relationship between communities of Geobacteraceae and environmental factors and geographic distance.

Results and discussion

Quantitative PCR showed that the abundance of 16S rRNA genes of Geobacteraceae ranged from (1.20?±?0.18)?×?10⁸ to 1.13?×?10⁹?±?2.25?×?10⁸ copies per gram of soil (dry weight) across different types of soils. Illumina sequencing results showed Geobacter was the dominant genus within the family of Geobacteraceae. Multivariate regression tree (MRT) analysis showed that soil amorphous iron contributed more (22.46 %) to the variation of dominant species of Geobacteraceae than other examined soil chemical factors such as pH (14.52 %), ammonium (5.12 %), and dissolved organic carbon (4.74 %). Additionally, more geographically distant sites harbored less similar communities. Variance partitioning analysis (VPA) showed that geographic distance contributed more to the variation of Geobacteraceae than any other factor, although the environmental factors explained more variation when combined. So, we detected the uneven distribution of Geobacteraceae in paddy soils of China and demonstrated that Geobacteraceae community composition was strongly associated with geographic distance and soil chemical factors including aFe, pH, Fe, DOC, C:N, and NO₃ ^?-N. These results greatly expand the knowledge of the distribution of Geobacteraceae in environments, particularly in terrestrial ecosystems.

Conclusions

Our results showed that geographic distance and amorphous iron played important roles in shaping Geobacteraceae community composition and revealed that both geographic distance and soil properties governed Geobacteraceae biogeography in paddy soils. Our findings will be critical in facilitating the prediction of element cycling by incorporating information on functional microbial communities into current biogeochemical models.

     

Abundance and diversity of sulphur-oxidising bacteria and their role in oxidising elemental sulphur in cropping soils

There is an increasing interest in elemental S as a S fertiliser source, but to be available to plants, elemental S has to be oxidised to sulphate. Elemental S oxidation is known to be affected by soil properties and environmental conditions, but it is still unclear if elemental S oxidation is related to the abundance and diversity of S-oxidising bacteria in cropping soils. In this study, we investigated the abundance and diversity of S-oxidising bacteria by targeting a functional gene (soxB) and assessed their relationship with elemental S oxidation in ten cropping soils. Positive correlations between soil C, N and S contents on the one hand and the abundances of soxB and 16S ribosomal deoxyribonucleic acid (rRNA) genes on the other suggested that the abundances of S oxidising bacteria in particular and of bacteria in general depend on soil C and nutrient supply. Both soxB and 16S rRNA gene abundances were significantly correlated with the oxidation rate of elemental S (P < 0.05). In addition, more than 80% of the variation in the oxidation rate of elemental S could be explained by the combination of soxB or 16S rRNA gene abundances and soil pH, suggesting that pH not only affected bacterial abundances but also their activity during elemental S oxidation. Clone libraries constructed with the soxB primers showed genera belonging to Alphaproteobacteria, Betaproteobacteria and Deltaproteobacteria and Actinobacteria. The phylogenetic diversity and relative distribution of soxB clones revealed great differences across soils. However, no direct linkage was found between the diversity of S-oxidising bacteria and elemental S oxidation rate.     

An improvement on the papadakis covariate to account for spatial variation

The Papadakis covariate is commonly used to account for spatial variation in agricultural field experiments. However, it is calculated from the observed yield, and is affected by unexpected land discontinuity. To address this problem, we propose two extensions. First, we introduce a kriged covariate which is based on spatial information in the field. Two covariates, namely the kriged residual and the kriged Papadakis residual, are discussed. The second extension is a modification of the conventional Papadakis covariate that assigns equal weight to neighboring plots, regardless of their distance from the point of interest. The proposed covariate (a modified Papadakis covariate) assigns different weights to plot yield according to their spatial position. The proposed extensions are compared to the conventional Papadakis covariate using field data from Ethiopia. Simulations were conducted to evaluate the performance of these covariates. The number of neighbors needed to compute the proposed covariate are determined by the range of the variogram.     

Erythromycin Exposure Disrupts the Life Cycle Stages of <Emphasis Type="Italic">Aedes aegypti</Emphasis> L. (Diptera: Culicidae)

Erythromycin is one of the most widely used antibiotics globally and is considered an emerging contaminant in wastewaters and environmental waters. The egg, larval, and pupal stages of the dengue vector Aedes aegypti L. reside and develop in aquatic environments. These mosquito stages may be exposed to compounds in the water, such as erythromycin. Aquatic stages of Ae. aegypti were reared in different concentrations of erythromycin which resulted in significant delay and decrease in eclosion of eggs and pupation of larvae (P?<?0.05). Moreover, emergence of adults from pupae, larval survival, and adult female fecundity significantly decreased (P?<?0.05). A few occurrences of hypopigmentation in larvae and blisters in adult mosquitoes were also observed. Interestingly, second-generation eggs, which were laid by adult female mosquitoes exposed to erythromycin during their aquatic stages, did not exhibit decreased levels of eclosion in the presence of erythromycin. These results reveal that long-term erythromycin exposure disrupts the Ae. aegypti life cycle by decreasing survival and delaying progression throughout different life stages. However, this study demonstrates that Ae. aegypti can rapidly acquire significant tolerance to the emerging environmental contaminant erythromycin within two generations.     

Abundance of transcripts of functional gene reflects the inverse relationship between CH<Subscript>4</Subscript> and N<Subscript>2</Subscript>O emissions during mid-season drainage in acidic paddy soil

Agricultural management significantly affects methane (CH₄) and nitrous oxide (N₂O) emissions from paddy fields. However, little is known about the underlying microbiological mechanism. Field experiment was conducted to investigate the effect of the water regime and straw incorporation on CH₄ and N₂O emissions and soil properties. Quantitative PCR was applied to measure the abundance of soil methanogens, methane-oxidising bacteria, nitrifiers, and denitrifiers according to DNA and mRNA expression levels of microbial genes, including mcrA, pmoA, amoA, and nirK/nirS/nosZ. Field trials showed that the CH₄ and N₂O flux rates were negatively correlated with each other, and N₂O emissions were far lower than CH₄ emissions. Drainage and straw incorporation affected functional gene abundance through altered soil environment. The present (DNA-level) gene abundances of amoA, nosZ, and mcrA were higher with straw incorporation than those without straw incorporation, and they were positively correlated with high concentrations of soil exchangeable NH₄⁺ and dissolved organic carbon. The active (mRNA-level) gene abundance of mcrA was lower in the drainage treatment than in continuous flooding, which was negatively correlated with soil redox potential (Eh). The CH₄ flux rate was significantly and positively correlated with active mcrA abundance but negatively correlated with Eh. The N₂O flux rate was significantly and positively correlated with present and active nirS abundance and positively correlated with soil Eh. Thus, we demonstrated that active gene abundance, such as of mcrA for CH₄ and nirS for N₂O, reflects the contradictory relationship between CH₄ and N₂O emissions regulated by soil Eh in acidic paddy soils.     

Niche partitioning based on soil type and climate at the landscape scale in a community of plant-feeding nematodes

Understanding how environmental factors structure communities is important in conservation biology and ecosystem management. The aim of this study was to test the hypothesis that a plant-feeding nematode community composed of six species is structured by soil type and climate at the landscape scale, and that niche partitioning via these factors is consistent with the coexistence of the species. Martinique has an impressive diversity of abiotic factors (climate and soil type) over a relatively small land area, which facilitates the study of how soil type and climate affect the nematode community.We conducted this study by building an extensive data set containing the abundance of each nematode species on banana (3708 samples and 5,673,705 nematodes) in a wide range of sites in Martinique. The data set also contained environmental data (soil, climate) and plantation age. We analyzed the response of each nematode species to climate and soil type with a generalized linear model in order to understand whether niche partitioning of factors could contribute to the coexistence of the nematode species.Temperature, rainfall, soil type, and plantation age significantly affected the abundance of the six nematode species. While some pairs of species shared the same environmental niches, other showed clear niche partitioning along climatic axes. The two dominant species, Radopholus similis and Helicotylenchus multicinctus, have similar convergent ecological niches regarding climate, soil type, plantation age, and host range. These two species, which often co-occur, probably have different resources at the root scale. Soil type and climate structure plant-feeding nematode species community at the island scale. Further studies need to evaluate coexistence at the root scale among dominant species.     

Long-term fertilisation regimes affect the composition of the alkaline phosphomonoesterase encoding microbial community of a vertisol and its derivative soil fractions

Alkaline phosphomonoesterase (ALP) mainly originates from soil microbial secretion and plays a crucial role in the turnover of soil phosphorus (P). To examine the response of ALP-encoding microbial communities (analysed for the biomarker of the ALP gene, phoD) of soils and derivative soil fractions to different fertilisation regimes, soil samples were collected from a long-term experimental field (over 35 years). The different organic P (Po) pools of soil fractions and the ALP activity of soil were also determined. Compared with chemical-only fertilised soils, the ALP activity was 232–815% higher in organic-amended soils, and the highest enzyme activity was observed in the organic-only fertilised treatment. The abundance of the phoD gene harbouring in soil fractions, determined by quantitative PCR (qPCR), was affected by different fertilisations. The highest abundance of the phoD gene was generally detected in the 2–63-μm-sized fraction (silt), but most phoD-encoding microbial species were associated to the 0.1–2-μm-sized fraction (clay) in the chemical-only fertilised soil. The contents of labile Po (LPo), moderately labile Po (MLPo) and fulvic acid-associated Po (FAPo) were significantly correlated with the phoD gene abundance, whereas only LPo content was significantly correlated with the ALP activity. The dominant phoD-encoding phylas were Actinobacteria and Proteobacteria, according to a high-throughput sequencing. Bradyrhizobium, a N₂-fixer identified as a phoD-encoding genus, showed the highest abundance in fertilised soils. The abundance of Bradyrhizobium, Streptomyces, Modestobacter, Lysobacter, Frankia and Burkholderia increased with the organic-only amendment and was significantly correlated with the ALP activity. According to structure equation models (SEM), pH and LPo content significantly and directly affected the ALP activity; the soil organic C (C_org) content was related to composition and abundances of phoD-harbouring microbial communities; since both microbial properties were correlated to the ALP activity, the C_org content was indirectly related to the ALP activity. In conclusion, soil management practices can be used to optimise the contents of soil available P and the organic P with regulation of soil ALP activity and the community composition of corresponding microbes.     

Population genetics of traditional landraces of <Emphasis Type="Italic">Cucurbita pepo</Emphasis> L., 1753 in the cloud forest in Baja Verapaz,Guatemala

Little is known regarding the effect of fragmentation and human agricultural management on the genetic variation and gene flow of Cucurbita pepo L., 1753 in moderate fragmented areas in central Guatemala. We hypothesize that the genetic variation of C. pepo is affected by forest fragmentation and by traditional agricultural management. Therefore, we aim to determine: (1) the genetic diversity and genetic structure of C. pepo in the Cloud Forest Corridor (CFC) (2) the extent of genetic admixture between commercial variety (CV) and traditional landraces (TL) of C. pepo, (3) the effect of habitat fragmentation in the population genetics of C. pepo with a landscape approach, and (4) the potential relationship between traditional management practices and genetic diversity of C. pepo in the CFC. We detected the existence of high level of genetic diversity (AR = 3.43; He = 0.50), inbreeding (Fis = 0.25) and moderate population structure of C. pepo in the CFC (Fst = 0.16). No correlation between landscape and genetics was found. Also, we found high genetic admixture between CV and TL. It seems that human practices, mainly related with seed exchange patterns, could affect genetic diversity of C. pepo in the CFC. C. pepo populations in the CFC are structured, with inbreeding, and show admixture with the CV, an aspect that could affect its genetic diversity. The agricultural management influenced the population genetics of C. pepo in the CFC, but the landscape did not. We suggest that special efforts should be made to preserve the diversity of this important indigenous food source for Guatemalan people as well as their management practices.     

Prediction of the effects of climate change on <Emphasis Type="Italic">Sechium edule</Emphasis> (Jacq.) Swartz varietal groups in Mexico

Climate change has significant impacts on biodiversity and, particularly, on agriculture. In this study, the impact of climate change on five varietal groups of Sechium edule, up to the year 2050, was determined through the application of the HadGEM2-CC model based on bioclimate layers. The varietal groups, nigrum minor, albus dulcis and nigrum xalapensis, will lose more than 50 % of their potential current distribution due to a high impact in both the rcp 45 and the rcp 85 scenarios. These two varietal groups also have a limited distribution, which makes them highly susceptible. In the case of nigrum spinosum, a loss under 50 % is predicted with scenario rcp 45. The varietal group that increases its distribution in 11 % is virens levis. The model forecasts significant impacts up to the year 2050; however, the groups evaluated present high genetic diversity and phenotypic plasticity which allow adapting to new conditions that may contribute to mitigating the effects of climate change.     

Introduced earthworm species exhibited unique patterns of seasonal activity and vertical distribution,and <Emphasis Type="Italic">Lumbricus terrestris</Emphasis> burrows remained usable for at least 7 years in hardwood and pine stands

It is difficult to obtain non-destructive information on the seasonal dynamics of earthworms in northern forest soils. To overcome this, we used a Rhizotron facility to compile 7 years of data on the activity of anecic (Lumbricus terrestris) and endogeic (Aporrectodea caliginosa complex) earthworms in two contrasting soil/plant community types. We hypothesized that L. terrestris burrows would be used for longer than a typical L. terrestris lifetime, and that the distribution and activity pattern of the two earthworm species would respond differently to changes in soil moisture and temperature. For 7 years we recorded earthworm distribution and activity state bi-weekly to a depth of 1.5 m, tracked L. terrestris burrows using images captured annually, and measured soil temperature and moisture. Activity and vertical distribution of earthworms was closely linked to earthworm species and soil temperature in the fall, winter and spring. Lumbricus terrestris typically remained active through the winter, whereas the A. caliginosa complex was more likely to enter an aestivation period. Activity of all earthworms decreased substantially in July and August when soil temperature was at its highest and soil moisture at its lowest for the year. Most L. terrestris burrows were used continuously and moved very little during the 7-year study, likely creating spatiotemporally stable hotspots of soil resources. The different patterns of response of these species to soil temperature and moisture suggests that endogeic earthworms are more likely than anecic earthworms to adjust activity states in response to climate change mediated shifts in soil moisture and temperature.     

Niche partition of phenanthrene-degrading bacteria along a <Emphasis Type="Italic">Phragmites australis</Emphasis> rhizosphere gradient

The rhizosphere is a critical interface for pollutant remediation in soils. Association between biodegradation of organic pollutants and spatial pattern of degraders along the rhizosphere gradient is, however, still unclear. This study investigated the phenanthrene-degrading bacterial consortia in a Phragmites australis rhizosphere using DNA-stable isotope probing (DNA-SIP). The relative abundance of Sphingomonadales in the ¹³C-labeled consortia decreased with the distance from roots, suggesting that its contribution in phenanthrene degradation was decreased with the distance from roots. Conversely, the relative abundance of Rhizobiales, Rhodobacterales, Lactobacillales, and Enterobacteriales in ¹³C-labeled consortia increased with the distance from roots, suggesting that their contributions in phenanthrene degradation were increased with the distance from roots. The linkage numbers of bacterial species in the co-occurrence network increased with the percentages of ¹³C-labeled reads, suggesting the critical role of syntrophic interactions for phenanthrene degraders. These results suggest the niche partition of phenanthrene degraders, which leaded to the non-linear variation of phenanthrene degradation rates along the rhizosphere gradient. These findings will help us to better understand rhizo degradation of organic pollutants and optimize bioremediation technology by achieving a trade-off among different degraders.