Variation in incubation effort during egg laying in the Mountain Bluebird and its association with hatching asynchrony

Females in many bird species reportedly begin incubation prior to clutch completion, but the nature of such incubation and the degree to which it varies among females remains undescribed for almost all species. We used continuous recording of nest‐cup temperatures to document incubation effort during egg laying at 57 Mountain Bluebird (Sialia currucoides) nests in a high‐elevation Wyoming population. We then asked whether such effort predicted the degree to which eggs hatch asynchronously. Although substantial egg heating could begin abruptly late in laying (previously reported as the norm for this species) or even after clutch completion, we found that most (>90%) females began incubation gradually, engaging in a few (usually 1–8), brief (<10 min) bouts of heating on the day they laid their first or second egg. Thereafter, females varied markedly in when they increased incubation effort and by how much. The onset of nocturnal incubation also varied, with females beginning to incubate at night after laying their prepenultimate, penultimate, or last egg and not always initially incubating through the night. As an index of the total amount of heat applied to eggs during laying, we calculated the cumulative number of degrees by which nest‐cup temperatures exceeded the threshold temperature required for embryonic development. This value varied by more than 150‐fold between nests and explained >50% of the variation in hatching asynchrony. Our results thus provide strong support for the widely held, but rarely tested, assumption that parent birds can have substantial control over the degree of hatching asynchrony by varying the amount of incubation done prior to clutch completion.     

Microbial infection affects egg viability and incubation behavior in a tropical passerine

Many avian species initiate incubation before clutch completion,which causes eggs to hatch asynchronously. This influences broodcompetitive dynamics and often results in nestling mortality.The prevailing hypotheses contend that parents incubate earlybecause asynchronous hatching provides fitness benefits to parentsor surviving offspring. An alternative idea is that early incubationis the best of a bad job because of the costs of delaying incubationto the viability of first-laid eggs. To explore this, we examinedthe potential for microbial infection, and the relative effectsof infection and suboptimal development temperatures on theviability of pearly-eyed thrasher (Margarops fuscatus) eggs.We exposed newly laid eggs for 5 days at either end of a tropicalaltitudinal gradient and cleaned shells of half the eggs toreduce microbial growth. Uncleaned eggs were infected more thanwere cleaned eggs, and infection was greater for eggs exposedat the cool, humid site than at the hot, less humid site. Parentallyincubated eggs, however, were not infected, suggesting thatincubation limits infection. The consequence of exposure toinfection and high ambient temperatures was a dramatic reductionin viability; cleaned eggs held at the cool site had the highesthatching success, which was significantly greater than for uncleanedeggs at this site and for cleaned eggs held at the hot site.This provides the first evidence that microbes can infect unincubatedeggs of a wild bird, and that infection and ambient temperatureact independently to reduce hatching success. These factorscould affect avian life-history strategies in diverse habitats.     

A new method for catching cavity‐nesting birds during egg laying and incubation

ABSTRACT The physiological condition of female birds during the egg‐laying and incubation periods is of considerable interest and yet is relatively understudied in wild birds, primarily due to the difficulty of catching birds during this period without causing nest desertion. We therefore developed a box‐net to capture cavity‐nesting birds using sections of a mist‐net placed around a metal cubic frame. We captured female Great Tits (Parus major) as they left nest boxes during the egg‐laying and incubation periods and measured desertion rates. Using box‐nets, we captured 108 of 119 (90%) females during egg laying and 10 of 12 (83%) during incubation. Our recapture rate over two consecutive days during incubation was 50% (5 of 10). Females not captured left nest boxes before we attempted to capture them, escaped through a hole in the mist‐net, or remained in nest boxes for more than 2 h, after which we ended capture attempts. Overall, 22% of egg‐laying females deserted, with desertion rates highest early in the egg‐laying period. Desertion rates of females captured using box‐nets did not differ from those of undisturbed females. One of 10 females captured in a box‐net deserted during the incubation period. Box‐nets are portable, can be set up and taken down quickly and easily, and could potentially be used with nest boxes or natural cavities at any height. Box‐nets are easy to construct and adaptable for use with an array of cavity‐nesting birds, and can be an important tool for studying female physiology during egg laying and incubation.     

Dietary carotenoid supplementation facilitates egg laying in a wild passerine

During egg laying, females face a trade‐off between self‐maintenance and investment into current reproduction, since providing eggs with resources is energetically demanding, in particular if females lay one egg per day. However, the costs of egg laying not only relate to energetic requirements, but also depend on the availability of specific resources that are vital for egg production and embryonic development. One of these compounds are carotenoids, pigments with immuno‐stimulatory properties, which are crucial during embryonic development. In this study, we explore how carotenoid availability alleviates this trade‐off and facilitates egg laying in a small bird species, the blue tit (Cyanistes caeruleus). Blue tits have among the largest clutch size of all European passerines and they usually lay one egg per day, although laying interruptions are frequent. We performed a lutein supplementation experiment and measured potential consequences for egg laying capacity and egg quality. We found that lutein‐supplemented females had less laying interruptions and thus completed their clutch faster than control females. No effects of treatment were found on the onset of egg laying or clutch size. Experimentally enhanced carotenoid availability did not elevate yolk carotenoid levels or egg mass, but negatively affected eggshell thickness. Our results provide hence evidence on the limiting role of carotenoids during egg laying. However, the benefits of laying faster following lutein supplementation were counterbalanced by a lower accumulation of calcium in the eggshell. Thus, even though single components may constrain egg laying, it is the combined availability of a range of different resources which ultimately determines egg quality and thus embryonic development.     

Uterine and eggshell structure and histochemistry in a lizard with prolonged uterine egg retention (Lacertilia,Scincidae, Saiphos)

The eggshell of lizards is a complex structure composed of organic and inorganic molecules secreted by the oviduct, which protects the embryo by providing a barrier to the external environment and also allows the exchange of respiratory gases and water for life support. Calcium deposited on the surface of the eggshell provides an important nutrient source for the embryo. Variation in physical conditions encountered by eggs results in a tradeoff among these functions and influences eggshell structure. Evolution of prolonged uterine egg retention results in a significant change in the incubation environment, notably reduction in efficiency of gas exchange, and selection should favor a concomitant reduction in eggshell thickness. This model is supported by studies that demonstrate an inverse correlation between eggshell thickness and length of uterine egg retention. One mechanism leading to thinning of the eggshell is reduction in size of uterine shell glands. Saiphos equalis is an Australian scincid lizard with an unusual pattern of geographic variation in reproductive mode. All populations retain eggs in the uterus beyond the embryonic stage at oviposition typical for lizards, and some are viviparous. We compared structure and histochemistry of the uterus and eggshell of two populations of S. equalis, prolonged egg retention, and viviparous to test the hypotheses: 1) eggshell thickness is inversely correlated with length of egg retention and 2) eggshell thickness is positively correlated with size of shell glands. We found support for the first hypothesis but also found that eggshells of both populations are surprisingly thick compared with other lizards. Our histochemical data support prior conclusions that uterine shell glands are the source of protein fiber matrix of the eggshell, but we did not find a correlation between size of shell glands and eggshell thickness. Eggshell thickness is likely determined by density of uterine shell glands in this species. J. Morphol., 2010. © 2010 Wiley‐Liss, Inc.     

Reduced reproductive performance associated with warmer ambient temperatures during incubation in a winter‐breeding,food‐storing passerine

Timing of reproduction can influence individual fitness whereby early breeders tend to have higher reproductive success than late breeders. However, the fitness consequences of timing of breeding may also be influenced by environmental conditions after the commencement of breeding. We tested whether ambient temperatures during the incubation and early nestling periods modulated the effect of laying date on brood size and dominant juvenile survival in gray jays (Perisoreus canadensis), a sedentary boreal species whose late winter nesting depends, in part, on caches of perishable food. Previous evidence has suggested that warmer temperatures degrade the quality of these food hoards, and we asked whether warmer ambient temperatures during the incubation and early nestling periods would be associated with smaller brood sizes and lower summer survival of dominant juveniles. We used 38 years of data from a range‐edge population of gray jays in Algonquin Provincial Park, Ontario, where the population has declined over 50% since the study began. Consistent with the “hoard‐rot” hypothesis, we found that cold temperatures during incubation were associated with larger brood sizes in later breeding attempts, but temperatures had little effect on brood size for females breeding early in the season. This is the first evidence that laying date and temperature during incubation interactively influence brood size in any bird species. We did not find evidence that ambient temperatures during the incubation period or early part of the nestling period influenced summer survival of dominant juveniles. Our findings provide evidence that warming temperatures are associated with some aspects of reduced reproductive performance in a species that is reliant on cold temperatures to store perishable food caches, some of which are later consumed during the reproductive period.     

Experimental evidence that egg color indicates female condition at laying in a songbird

The signaling hypothesis of eggshell coloration in birds isbased on the assumption that females of species with blue-greeneggs signal their phenotypic quality to their mates throughdeposition of the antioxidant biliverdin as pigment. Egg pigmentationmay be an expression of the condition of females at laying orof genetic linkages between egg color and female performancevariables. We have supplemented 16 pied flycatcher, Ficedulahypoleuca, females with mealworms before and during laying andcompared the mass and color of their eggs as measured on theday of laying to those of 16 control females with the same nestconstruction and laying dates and clutch sizes. Supplementedfemales laid significantly heavier and more intensely blue-greeneggs than control females. Egg blue-green chroma was significantlyassociated with the amount of biliverdin in eggshells. Egg color,and thus biliverdin content, is an expression of female conditionat laying.     

Unpredictable perturbation reduces breeding propensity regardless of pre‐laying reproductive readiness in a partial capital breeder

Theoretically, individuals of migratory species should optimize reproductive investment based on a combination of timing of and body condition at arrival on the breeding grounds. A minimum threshold body mass is required to initiate reproduction, and the timing of reaching this threshold is critical because of the trade‐off between delaying breeding to gain in condition against the declining value of offspring with later reproductive timing. Long‐lived species have the flexibility within their life history to skip reproduction in a given year if they are unable to achieve this theoretical mass threshold. Although the decision to breed or not is an important parameter influencing population dynamics, the mechanisms underlying this decision are poorly understood. Here, we mimicked an unpredictable environmental perturbation that induced a reduction in body mass of Arctic pre‐breeding (before the laying period) female common eiders Somateria mollissima; a long‐lived migratory seaduck, while controlling for individual variation in the pre‐laying physiological reproductive readiness via vitellogenin (VTG) – a yolk‐targeted lipoprotein. Our aim was to causally determine the interaction between body condition and pre‐laying reproductive readiness (VTG) on breeding propensity by experimentally reducing body mass in treatment females. We first demonstrated that arrival body condition was a key driver of breeding propensity. Secondly, we found that treatment and VTG levels interacted to influence breeding propensity, indicating that our experimental manipulation, mimicking an unpredictable food shortage, reduced breeding propensity, regardless of the degree of pre‐laying physiological reproductive readiness (i.e. timing of ovarian follicles recruitment). Our experiment demonstrates that momentary environmental perturbations during the pre‐breeding period can strongly affect the decision to breed, a key parameter driving population dynamics.     

Extended incubation recesses by alpine‐breeding Horned Larks: a strategy for dealing with inclement weather?

ABSTRACT Incubating birds can incur high energetic costs and, when faced with a trade‐off between incubation and foraging, parents may neglect their eggs in favor of their own somatic needs. Extended incubation recesses are an example of neglect, but they are often treated as outliers and largely overlooked in studies of incubation behavior. We studied incubation rhythms of Horned Larks (Eremophila alpestris) on Hudson Bay Mountain, British Columbia, Canada, during four breeding seasons. Incubation recesses averaged 10.92 ± 0.38 min (N= 4076 2‐h periods), but we observed 70 extended recesses, ranging from 59 to 387 min in duration, at 35 nests. Although rare (<1% of all daytime recesses), extended recesses occurred in all 4 yr, were longer and more frequent in colder years (60% occurred in the two coldest years), and often occurred during inclement weather (39% occurred during three storm events). Extended recesses did not appear to compensate for long attendance periods because extended recess duration was not correlated with the duration of previous on‐bouts (P= 0.10, N= 70) or the mean on‐bout duration of the previous 2‐h period (P= 0.36, N= 70). Rather, extended recesses seemed to reflect a shift in parental investment away from their eggs and toward self‐maintenance when faced with energetically stressful conditions. Extended recesses may have reduced embryo viability; egg‐hatching rates were 91 ± 2.4% for nests where females did not take extended recesses and 81 ± 4.2% for nests where females did take extended recesses (P= 0.02, N= 56 nests). Extended recesses during incubation are rare events, but they may represent an important mechanism that allows birds to breed successfully in energetically challenging conditions.     

Spatio‐temporal variation in Helicoverpa egg parasitism by Trichogramma in a tropical Bt‐transgenic cotton landscape

• 1 Understanding the spatio‐temporal dynamics of insects in agroecosystems is crucial when developing effective management strategies that emphasize the biological control of pests.
• 2 Wild populations of Trichogramma Westwood egg parasitoids are utilized for the biological suppression of the potentially resistant pest species Helicoverpa armigera (Hübner) in Bt‐transgenic cotton Gossypium hirsutum L. crops in the Ord River Irrigation Area (ORIA), Western Australia, Australia.
• 3 Extensive, spatially‐stratified sampling during a season of relatively high Trichogramma abundance found that spatial patterns of pest egg parasitism in the ORIA tend toward heterogeneity, and do not necessarily coincide with host spatio‐temporal dynamics. Both patterns of host egg density and mean rates of parasitism are not good indicators of parasitoid spatio‐temporal dynamics in ORIA cotton crops.
• 4 Parasitism rates can be significantly higher within the middle strata of the cotton plant canopy before complete canopy closure, despite a similar number of host eggs being available elsewhere in the plant.
• 5 Spatial variation in egg parasitism by Trichogramma in Bt‐transgenic cotton is evident at the between‐field, within‐field and within‐plant scale, and is not solely driven by host spatial dynamics. These factors should be considered when estimating Trichogramma impact on pest species during biological control and spatio‐temporal studies of host‐parasitoid interactions in general.

     

Intraspecific variability in egg maturation patterns and associated life‐history trade‐offs in a polyembryonic parasitoid wasp

1. Life‐history theory predicts a trade‐off between the resources allocated to reproduction and those allocated to survival. Early maturation of eggs (pro‐ovigeny) is correlated with small body size and low adult longevity in interspecific comparisons among parasitoids, demonstrating this trade‐off. The handful of studies that have tested for similar correlations within species produced conflicting results. 2. Egg maturation patterns and related life‐history traits were studied in the polyembryonic parasitoid wasp, Copidosoma koehleri (Hymenoptera: Encyrtidae). Although the genus Copidosoma was previously reported to be fully pro‐ovigenic, mean egg loads of host‐deprived females almost doubled within their first 6 days of adulthood. 3. The initial egg‐loads of newly emerged females were determined and age‐specific realised fecundity curves were constructed for their clone‐mate twins. The females' initial egg loads increased with body size, but neither body size nor initial egg load was correlated with longevity and fecundity. 4. The variation in initial egg loads was lowest among clone‐mates, intermediate among non‐clone sisters and highest among non‐sister females. The within‐clone variability indicates environmental influences on egg maturation, while the between‐clone variation may be genetically based. 5. Ovaries of host‐deprived females contained fewer eggs at death (at ～29 days) than on day 6. Their egg loads at death were negatively correlated with life span, consistent with reduced egg production and/or egg resorption. Host deprivation prolonged the wasps' life span, suggesting a survival cost to egg maturation and oviposition. 6. It is concluded that adult fecundity and longevity were not traded off with pre‐adult egg maturation.     

Millimeter‐scale genetic gradients and community‐level molecular convergence in a hypersaline microbial mat

To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter‐scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near‐identical and acid‐shifted isoelectric point profiles due to a molecular convergence of amino‐acid usage, indicating that hypersalinity enforces an overriding selective pressure on the mat community.     

A quadratic correlation between long‐term mean group size and group density in a cooperatively breeding passerine

Both mean group size (MGS) and mean group density (MGD) are critical indices to characterize a population of cooperatively breeding birds. When a population reaches its carrying capacity, both long‐term MGS and long‐term MGD will remain relatively stable. However, there has been little study of how these two variables relate. The Masked laughingthrush Garrulax perspicillatus is a cooperatively breeding bird living in fragmented habitats. During 2010 and 2012‐2016, we used song playback to observe and confirm the group sizes and territory ranges of the birds and the data of bird presence to determine habitat suitability. By grouping the nearest territories according to their geographical coordinates, we divided the whole study area into 12 subareas and the whole population into 12 subpopulations. Then, we calculated both MGS and MGD for different time durations for each subpopulation. Finally, using MGD as independent variable and MGS as the dependent variable, we explored the correlations between MGS and MGD by fitting quadratic functions and modeling quadratic regression. Both MGS and MGD were averaged for different time durations and were cross‐related. Our results show that the MGS for more than 2 years significantly correlated with MGD for more than 3 years in a reverse parabolic shape, differing from that of short‐term effects. Our findings suggest that long‐term MGD is a better predictor of long‐term habitat quality and that long‐term MGS is determined by long‐term habitat quality in Masked Laughingthrushes. Based on above findings, we can infer that: (1) Long‐term habitat quality determines the long‐term MGS, but it sets no prerequisite for the status and source of group members; (2) Long‐term MGS in certain populations is adapted to the corresponding level of long‐term habitat quality, it facilitates us to predict the helper effects on current or future survival or reproduction in different situations. These findings and inferences are both helpful for us to understand the evolution of cooperative breeding.     

Melanin coloration has temperature‐dependent effects on breeding performance that may maintain phenotypic variation in a passerine bird

Fluctuating selection pressure may maintain phenotypic variation because of different types of individuals being adapted to different environmental conditions. We show that the extensive variation in the coloration of male pied flycatchers (Ficedula hypoleuca) can be maintained through differences in the reproductive success of male phenotypes under different conditions. The effects of weather conditions on the relative success of different male phenotypes varied between different phases of breeding. The reproductive output of black males was the highest when it was cold during egg‐laying but warm during the nestling period, whereas the fledgling production of brown males was highest when it was continuously warm. In addition, male forehead and wing patch sizes had context‐dependent effects on timing of breeding and nestling mortality, respectively. These results indicate that environmental heterogeneity plays a role in maintaining phenotypic variation. As melanin‐based coloration is heritable, climate change may alter phenotype frequencies depending on the patterns of warming.     

Associations between redox‐sensitive trace metals and microbial communities in a Proterozoic ocean analogue

Constraints on Precambrian ocean chemistry are dependent upon sediment geochemistry. However, diagenesis and metamorphism can destroy primary biosignatures, making it difficult to consider biology when interpreting geochemical data. Modern analogues for ancient ecosystems can be useful tools for identifying how sediment geochemistry records an active biosphere. The Middle Island Sinkhole (MIS) in Lake Huron is an analogue for shallow Proterozoic waters due to its low oxygen water chemistry and microbial communities that exhibit diverse metabolic functions at the sediment–water interface. This study uses sediment trace metal contents and microbial abundances in MIS sediments and an oxygenated Lake Huron control site (LH) to infer mechanisms for trace metal burial. The adsorption of trace metals to Mn‐oxyhydroxides is a critical burial pathway for metals in oxic LH sediments, but not for the MIS mat and sediments, consistent with conventional understanding of Mn cycling. Micronutrient trace metals (e.g., Zn) are associated with organic matter regardless of oxygen and sulfide availability. Although U and V are conventionally considered to be organically complexed in suboxic and anoxic conditions, U and organic covary in oxic LH sediments, and Mn‐oxyhydroxide cycling dominates V deposition in the anoxic MIS sediments. Significant correlations between Mo and organic matter across all redox regimes have major implications for our interpretations of Mo isotope systematics in the geologic record. Finally, while microbial groups vary between the sampling locales (e.g., the cyanobacteria in the MIS microbial mat are not present in LH sediments), LH and MIS ultimately have similar relationships between microbial assemblages and metal burial, making it difficult to link trace metal burial to microbial metabolisms. Together, these results indicate that bulk sediment trace metal composition does not capture microbiological processes; more robust trace metal geochemistry such as isotopes and speciation may be critical for understanding the intersections between microbiology and sediment geochemistry.     

Diversity decoupled from sulfur isotope fractionation in a sulfate‐reducing microbial community

The extent of fractionation of sulfur isotopes by sulfate‐reducing microbes is dictated by genomic and environmental factors. A greater understanding of species‐specific fractionations may better inform interpretation of sulfur isotopes preserved in the rock record. To examine whether gene diversity influences net isotopic fractionation in situ, we assessed environmental chemistry, sulfate reduction rates, diversity of putative sulfur‐metabolizing organisms by 16S rRNA and dissimilatory sulfite reductase (dsrB) gene amplicon sequencing, and net fractionation of sulfur isotopes along a sediment transect of a hypersaline Arctic spring. In situ sulfate reduction rates yielded minimum cell‐specific sulfate reduction rates < 0.3 × 10^?15 moles cell^?1 day^?1. Neither 16S rRNA nor dsrB diversity indices correlated with relatively constant (38‰–45‰) net isotope fractionation (ε³⁴S_{sulfide‐sulfate}). Measured ε³⁴S values could be reproduced in a mechanistic fractionation model if 1%–2% of the microbial community (10%–60% of Deltaproteobacteria) were engaged in sulfate respiration, indicating heterogeneous respiratory activity within sulfate‐reducing populations. This model indicated enzymatic kinetic diversity of Apr was more likely to correlate with sulfur fractionation than DsrB. We propose that, above a threshold Shannon diversity value of 0.8 for dsrB, the influence of the specific composition of the microbial community responsible for generating an isotope signal is overprinted by the control exerted by environmental variables on microbial physiology.     

Water quality during egg incubation influences yolk-sac fry sodium kinetics in Atlantic salmon, Salmo salar L.: a possible mechanism of adaptation to acid waters

Atlantic salmon ( Salmo salar L.) fry hatched from eggs transferred from high-Na to low-Na water during the eyed stage of development had a significantly higher V_max and lower K_m (P <0.01) of the sodium uptake mechanism than fry hatched from eggs incubated entirely in low-Na or high-Na water.
Fry hatched from eggs transferred to acid, high aluminium water during the eyed stage of development had a similar V_max and K_m to fry hatched from eggs incubated entirely in high- or low-Na water. Eggs incubated continuously in acid, high aluminium (low-Na) water produced fry with significantly lower K_m and V_max values than fry hatched from eggs incubated continuously in low-Na water. Eggs and fry in acid, high aluminium water continually lost sodium and mortality was 100% at 5 5 M O degree-days (2–3 weeks after hatching).
The results are discussed with respect to the influence of perivitelline fluid ion activities in eggs in acid, high aluminium water on the kinetic characteristics of sodium uptake in yolk-sac fry. A possible mechanism for the long-term adaptation of teleosts in acidified natural waters is also proposed.     

Changes in impact of HLA class I allele expression on HIV‐1 plasma virus loads at a population level over time

HLA class I allele types have differential impacts on the level of the pVL and outcome of HIV‐1 infection. While accumulations of CTL escape mutations at population levels have been reported, their actual impact on the level of the pVL remains unknown. In this study HLA class I types from 141 untreated, chronically HIV‐1 infected Japanese patients diagnosed from 1995–2007 were determined, and the associations between expression of individual HLA alleles and level of pVL analyzed. It was found that the Japanese population has an extremely narrow HLA distribution compared to other ethnic groups, which may facilitate accumulation of CTL escape mutations at the population level. Moreover while they uniquely lack the most protective HLA‐B27/B57, they commonly express the alleles that are protective in Caucasians (A11:10.4%, A26:11.55%, B51:8.6% and Cw14:12.7%). Cross‐sectional analyses revealed no significant associations between expression of individual alleles and the level of the pVL. The patients were then stratified by the date of HIV diagnosis and the analyses repeated. It was found that, before 2001, B51+ individuals displayed significantly lower pVL than the other patients (median: 5150 vs. 18 000 RNA copies/ml, P= 0.048); however thereafter this protective effect waned and disappeared, whereas no changes were observed for any other alleles over time. These results indicate that, at a population level, some HLA alleles have been losing their beneficial effects against HIV disease progression over time, thereby possibly posing a significant challenge for HIV vaccine development. However such detrimental effects may be limited to particular HLA class I alleles.     

Long‐term balanced fertilization increases the soil microbial functional diversity in a phosphorus‐limited paddy soil

The influence of long‐term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22‐year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array‐based analysis revealed that long‐term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer‐induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P‐limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions.     

Effect of long‐term mineral fertilisation on soil microbial abundance,community structure and diversity in a Typic Hapludoll under intensive farming systems

Fertiliser application can not only influence plant communities, but also the soil microbial community dynamics, and consequently soil quality. Specifically, mineral fertilisation can directly or indirectly affect soil chemical properties, microbial abundance and, the structure and diversity of soil microbial communities. We investigated the impact of six different mineral fertiliser regimes in a maize/soybean rotation system: control (CK, without fertilisation), PS (application of phosphorus plus sulphur), NS (application of nitrogen plus S), NP (application of N plus P), NPS (application of N, P plus S) and NPSm (application of N, P, S plus micronutrients). Soil samples were collected at the physiological maturity stage of maize and soybean in March of 2013 and 2014, respectively. Overall, mineral fertilisation resulted in significantly decreased soil pH and increased total organic carbon compared with the control (CK). The analysis of terminal restriction fragment length polymorphism (T‐RFLP) revealed that mineral fertilisers caused a shift in the composition of both bacterial and fungal communities. In 2013, the highest value of Shannon diversity of bacterial terminal restriction fragments (TRFs) was found in control soils. In 2014, NPSm treated soils showed the lowest values of diversity for both bacterial and fungal TRFs. In both crop growing seasons, the analysis of phospholipid fatty acid (PLFA) detected the lowest value of total microbial biomass under CK. As PLFA analysis can be used to evaluate total microbial community, this result suggests that fertilisation increased total microbial biomass. When the bacterial and fungal abundance were examined using real time polymerase chain reaction, the results revealed that mineral fertilisation led to decreased bacterial abundance (16S rRNA), while fungal abundance (18S rRNA) was found to be increased in both crop growing seasons. Our results show that mineral fertiliser application has a significant impact on soil properties, bacterial and fungal abundance and microbial diversity. However, further studies are needed to better understand the mechanisms involved in the changes to microbial communities as a consequence of mineral fertilisation.