劉肖應(yīng),李 瑩,耿家亙,汪 杰,陳 清,李 思,2*
施肥模式對設(shè)施土壤抗生素及抗性基因的影響
劉肖應(yīng)1,李 瑩1,耿家亙1,汪 杰1,陳 清1,李 思1,2*
(1.中國農(nóng)業(yè)大學(xué)資源與環(huán)境學(xué)院,農(nóng)田土壤污染防控與修復(fù)北京市重點實驗室,北京 100193;2.中國農(nóng)業(yè)大學(xué)煙臺研究院,山東 煙臺 264670)
采集不同施肥模式下設(shè)施菜地表層土壤(0~20cm),對83種抗生素和203種抗性基因(ARGs)進行檢測.結(jié)果表明,各處理組土壤中共檢出14種抗生素、129種ARGs亞型和10種可移動遺傳元件(MGEs).四環(huán)素類(TCs)是土壤中殘留的主要抗生素,β-內(nèi)酰胺類和多重耐藥類抗性基因是主要的ARGs,放線菌門(Actinobacteria)、變形菌門(Proteobacteria)、綠彎菌門(Chloroflexi)和厚壁菌門(Firmicutes)是主要的細菌門.施肥增加了土壤中抗生素殘留和ARGs的多樣性及豐度,并且提高了土壤細菌群落多樣性.施用常量有機肥組抗生素、ARGs和MGEs相對豐度最大,有機肥減量可有效降低抗生素和ARGs污染程度,稻殼還田對控制抗生素和ARGs污染具有積極作用.設(shè)施菜地土壤中抗生素選擇壓力、細菌群落結(jié)構(gòu)變化和MGEs是影響ARGs分布的驅(qū)動因素.
抗生素;抗生素抗性基因;抗性機制;微生物多樣性;設(shè)施土壤
抗生素污染以及抗生素抗性基因(ARGs)的形成和傳播是21世紀(jì)威脅人類健康的首要因素之一[1].中國是全球抗生素生產(chǎn)和使用大國,我國獸用抗生素使用量約占抗生素使用總量的52%[2].然而,抗生素被畜禽攝入后無法被完全吸收,約有30%~90%的抗生素以原藥和代謝物的形式通過糞便或尿液排出體外[3],導(dǎo)致環(huán)境中抗生素和ARGs的積累.
畜禽糞肥施用是設(shè)施土壤中抗生素和ARGs的重要來源.與露天菜地相比,設(shè)施菜地單位種植面積的施肥量顯著提高,造成設(shè)施土壤中抗生素[3-5]和ARGs[4,6]污染的加劇.與露天土壤相比,我國20個省份51個設(shè)施土壤中抗生素和ARGs的污染水平顯著升高,設(shè)施土壤中四環(huán)素類(TCs)、喹諾酮類(QNs)和磺胺類(SAs)抗生素的平均濃度分別是露天土壤的2.28倍、2.15倍和0.25倍,設(shè)施菜地土壤中ARGs相對豐度提高了近一倍[4].
施肥模式可顯著影響設(shè)施菜地土壤中抗生素和ARGs的賦存.與不施肥相比,施用化肥和有機肥可改變土壤理化性質(zhì)[7],影響土壤細菌群落結(jié)構(gòu)[8],顯著增加土壤中抗生素[9]和ARGs的豐度[7,10].作物秸稈作為土壤改良劑,秸稈還田可降低土壤中ARGs的相對豐度[10-11].土壤中抗生素抗性菌(ARB)攜帶的ARGs可通過質(zhì)粒等可移動遺傳元件(MGEs)水平轉(zhuǎn)移到土著細菌中[12-13],對土壤生態(tài)系統(tǒng)和人類健康構(gòu)成潛在威脅.
目前,有關(guān)不同施肥模式下設(shè)施土壤中抗生素和ARGs賦存情況的研究相對較少.因此,本文以設(shè)施土壤為研究對象,考察不同施肥模式對土壤中抗生素、細菌群落、ARGs和MGEs的影響,為設(shè)施土壤中抗生素和ARGs的污染控制提供理論支撐.
試驗地點位于山東省壽光市蔬菜標(biāo)準(zhǔn)中心基地(36°55'N,118°45'E),種植作物為番茄.棚高為6.5m,總面積為960m2,日平均溫度為25℃,日平均濕度為65%,日平均二氧化碳濃度為650mL/m3,實驗開始于2020年8月,2021年1月番茄收獲后采集土壤樣品.共設(shè)6個處理組,分別為:(1)不施肥(CK);(2)單施化肥(F):氮(N)、磷(P2O5)和鉀(K2O)投入量分別為300,120和550kg/hm2;(3)單施有機肥(M):腐熟雞糞,用量為20t/hm2;(4)化肥配施(FM):F+M;(5)化肥配施有機肥減量(FLM):在F處理組基礎(chǔ)上,雞糞用量減少為M組的1/6;(6)化肥配施有機肥減量增碳(FLMS):在FLM處理組基礎(chǔ)上增施20t/hm2稻殼.6個處理組面積均為88.2m2,每個處理設(shè)置3個重復(fù),采用隨機區(qū)組排列.栽培模式為傳統(tǒng)的雙行壟栽,壟寬80cm,壟間距50cm,番茄株距40cm.雞糞和稻殼在作物種植前均勻撒施后翻耕作為基肥,化肥在作物灌溉季隨灌溉水沖施,澆水情況根據(jù)設(shè)置的灌溉下限(田間持水量的70%)進行自動灌溉.番茄收獲后其作物殘茬全部移出溫室.
采用5點采樣法采集6個處理組表層土壤(0~20cm),每個處理采集3個平行樣,將平行樣混合進行后續(xù)測試.去除植物根莖、砂礫石塊等后裝入鋁箔袋,在干冰保護下盡快運回實驗室.一部分土樣經(jīng)風(fēng)干、磨碎過2mm篩,用于土壤基本理化性質(zhì)的測定(結(jié)果如表1所示),包括土壤pH值和有機質(zhì)含量;其余土樣分別于-20和-80℃保存,用于抗生素測定和DNA提取.
表1 不同施肥模下土壤的理化性質(zhì)
根據(jù)文獻調(diào)研,土壤中抗生素提取和分析采用超聲提取-固相萃取-超高效液相色譜-串聯(lián)質(zhì)譜法[14-17].目標(biāo)抗生素共7類83種,包括22種SAs、16種QNs、13種TCs、15種β-Ls (β-內(nèi)酰胺類)、10種MLs (大環(huán)內(nèi)酯類)、5種PEs (聚醚類)和2種LMs (林可霉素類).稱取5g土樣,加入10mL提取液(檸檬酸緩沖液(pH=3)和乙腈,體積比為1:1)和50ng抗生素內(nèi)標(biāo)超聲提取3次,合并上清液后用超純水稀釋至500mL,經(jīng)HLB小柱(500mg, 6mL, Waters, USA)凈化富集,然后用甲醇進行洗脫,氮吹至近干后,再用甲醇定容至1mL,過0.22μm濾膜后于-20℃保存待測.抗生素檢測采用的流動相為甲醇和含0.1%(體積分?jǐn)?shù))甲酸的超純水,進樣量為5μL,質(zhì)譜采用正離子模式.方法加標(biāo)回收率為67.2%~129%,檢出限為0.001~0.14ng/g[15].
土壤DNA提取后,通過瓊脂糖凝膠電泳和Nanodrop微量分光光度計對DNA進行質(zhì)量和濃度評估,使用Illumina MiSeq平臺測序,上述步驟均由上海美吉生物醫(yī)藥科技有限公司完成.生物信息學(xué)分析在美吉平臺生物云(http://www.i-sanger.com)進行.
采用Wafergen智能芯片超高通量PCR系統(tǒng)定量檢測203種ARGs(多重耐藥類、大環(huán)內(nèi)酯類-林可霉素類-鏈霉素類(MLS)、磺胺類、四環(huán)素類、β-內(nèi)酰胺類、氯霉素類和多粘菌素類)和11種MGEs(8種轉(zhuǎn)座酶基因和3種整合酶基因),共設(shè)置216對引物,其中包括1對16S rRNA內(nèi)參引物.反應(yīng)體系為1 ×LightCycler 480SYBR Gree I Master,DNA模板濃度2ng/μL,引物濃度為500nmol/L,反應(yīng)體系100nL. PCR反應(yīng)程序為:預(yù)變性95℃下10min,然后95℃下30s,60℃下30s共進行40個循環(huán)[10].
采用Origin 2019b繪制柱狀圖;使用R軟件(v4.1.2)pheatmap包繪制熱圖,ggplot2包繪制冗余分析圖;igraph包構(gòu)建共現(xiàn)網(wǎng)絡(luò),并利用Gephi(v0.9.2)可視化.
不同施肥模式設(shè)施菜地土壤樣品中共檢出15種抗生素,包括3種QNs、6種TCs、4種MLs和2種PEs,它們的總濃度為2.95~12.70μg/kg(圖1),與山東省不同種植年限設(shè)施菜地中抗生素濃度相當(dāng)[18],遠低于北京市11個溫室土壤中的抗生素濃度(28~ 1051μg/kg)[3].從組成來看,主要的抗生素為強力霉素(1.78~8.81μg/kg)、脫水紅霉素(0.44~1.15μg/kg)和噁喹酸(0.32~0.80μg/kg) (圖1).這3種抗生素的濃度分別與珠三角地區(qū)某蔬菜生產(chǎn)基地土壤[19]、珠江口典型水產(chǎn)養(yǎng)殖區(qū)沉積物[20]以及河北石家莊土壤中抗生素的濃度水平相當(dāng)[21].
施肥模式
與CK和F處理組相比,施用常量有機肥組(M和FM)和減量有機肥組(FLM和FLMS)中,TCs類抗生素濃度由0.86~1.31μg/kg分別增加至6.78~ 9.89μg/kg和2.27~3.13μg/kg,可見雞糞施用增加了TCs濃度,這與其他研究結(jié)果一致[3,22],主要是由于TCs類抗生素是畜禽養(yǎng)殖中使用量最大的一類抗生素,并且它們在土壤顆粒上的吸附能力較強[23].雞糞中TCs類的總濃度為43.47μg/kg,因此有機肥施用是土壤抗生素的重要來源[24],而減量施用有機肥可有效降低土壤中抗生素殘留.從TCs類組成來看,金霉素在腐熟雞糞中的含量最高(30.58μg/kg),但在處理組土壤中未檢出,土壤中檢出了3種金霉素的轉(zhuǎn)化產(chǎn)物,包括脫水金霉素、差向脫水金霉素和4-差向金霉素,研究表明差向異構(gòu)化是金霉素在環(huán)境中的主要降解過程[25].因此,除抗生素母體外,環(huán)境中抗生素降解產(chǎn)物的賦存和毒性也應(yīng)引起關(guān)注.
PEs類抗生素是養(yǎng)雞業(yè)中廣泛用于治療雞球蟲病的一種離子載體類藥物[26],本研究雞糞樣品中檢出2種PEs類抗生素,其中莫能菌素的濃度高達1081μg/kg,與牛糞中的值(1351μg/kg)[27]相當(dāng),低于肉雞糞便中的值(5.60mg/kg)[28].與腐熟雞糞相比,各處理組土壤中PEs濃度顯著降低,可能是因為有氧條件下PEs在土壤中的降解速率較快[29].研究發(fā)現(xiàn)莫能菌素以1mg/kg初始濃度施入土壤時,一個月內(nèi)便會消散,半衰期僅3.3d[30].此外,SAs類抗生素僅在雞糞中檢出,在土壤中未檢出,這可能與磺胺類抗生素水溶性較大而在土壤中吸附較弱有關(guān)[31].
各處理組土壤中共檢出66~81種ARGs,其中MLS類和四環(huán)素類ARGs數(shù)目最多(圖2(a)).ARGs和MGEs的相對豐度分別為9.23′10-2~1.61′10-1copies/16S rRNA gene copies和5.90×10-3~1.48× 10-2copies/16S rRNA gene copies(圖2(b)).從ARGs組成來看,β-內(nèi)酰胺類和多重耐藥類豐度最大,占各處理組總豐度的51.13%~71.62%和20.60%~35.34%,與其他施肥研究結(jié)果相似[32-34].抗生素失活和外排泵是最主要的抗性機制(圖2(c)),與其他研究結(jié)果一致[35-36].
不同施肥模式下,與CK和F處理組相比,有機肥施用增加了土壤中ARGs的多樣性和豐度.CK組和F組土壤中ARGs的Shannon指數(shù)為1.26和1.15,而在M組和FM組分別升高至1.51和1.73與CK組相比,M組ARGs總豐度增加了68%,這與其他研究結(jié)果一致[6,37].主要是由于動物源有機肥中含有大量ARGs,施入設(shè)施菜地后,一方面向土壤中引入了外來ARGs,另一方面有機肥可以促進土壤細菌群落生長,促進ARGs在細菌群落之間的水平轉(zhuǎn)移,致使土壤中內(nèi)源ARGs富集[32,34].與CK相比,有機肥減量處理組(FLM和FLMS)中ARGs豐度分別增加了33.89%和30.81%,但低于M組,說明有機肥減量可以有效緩解ARGs污染.加入稻殼后,與FLM組比,FLMS組中ARGs相對豐度略有下降,這與已有研究結(jié)果相似[38].同時,與CK相比,施肥增加了土壤中MGEs的種類(圖2(a))和豐度(圖2(b)),因此,施肥增加了ARGs水平基因轉(zhuǎn)移的風(fēng)險[39].
施肥模式
6個處理組土壤中共檢出129種ARGs,其中32種在各處理組均有檢出(圖3(a)),它們占ARGs總豐度的70.7%~80.6%.從組成來看,TEM和F是兩種主要的ARGs(圖3(b)),研究表明,這兩種ARGs在雞糞、豬糞、牛糞、土壤、城市廢水及污泥、甚至飲用水中均有檢出[30,40-42],可能意味著它們在環(huán)境中普遍存在.轉(zhuǎn)座酶基因A-04和整合酶基因Ⅰ-1是兩種主要的MGEs,在各處理組土壤均有檢出(圖3(b)).
不同施肥模式下,M組土壤中F、A1和L/H-02基因的相對豐度較CK組增加了12~19倍,同時新增1、C、A-02和A(圖3(b)),表明有機肥施用促進了土壤中多種ARGs的富集[43].同時,與CK相比,施肥增加了A-04和Ⅰ-1的相對豐度,增加了ARGs水平轉(zhuǎn)移的風(fēng)險.與M和FM組相比,有機肥減量處理組(FLM和FLMS)中共有12種ARGs豐度降低,包括5種四環(huán)素類(G-02、L-02、G-01、L-01和Q)、3種MLS類(B-02、A和F)、3種多重耐藥類(Edelta1-02、R和Edelta1-01)和1種磺胺類(2),表明有機肥減量處理有利于削減土壤中ARGs污染.與FLM組相比,FLMS組TCs類和MLS類ARGs相對豐度下降,同時,MGEs相對豐度下降,表明秸稈還田對ARGs風(fēng)險傳播具有一定的阻控作用,這可能與FLMS組中有機質(zhì)含量較FLM組增加有關(guān)(表1),研究發(fā)現(xiàn)秸稈還田后有機質(zhì)對ARGs消除有積極作用[44].
抗生素的抗菌活性可抑制土壤微生物的生長,從而影響土壤微生物群落組成,這可能會導(dǎo)致土壤生態(tài)功能的改變[45].與CK相比,常規(guī)施肥處理組中Chao1指數(shù)和Shannon指數(shù)均升高,表明施肥增加了土壤細菌群落的多樣性(表2).可能是由于施肥可以增加土壤中有機質(zhì)含量,提高土壤養(yǎng)分水平,從而促進土壤微生物的生長[12].與FM組相比,FLM組中Chao1指數(shù)和Shannon指數(shù)降低,但施用稻殼后, FLMS組中Shannon指數(shù)上升,可能是由于稻殼還田能夠為土壤微生物提供豐富的碳源[11,13],從而提高土壤細菌群落的多樣性.
不同施肥模式對土壤細菌群落結(jié)構(gòu)的影響見圖4.放線菌門(Actinobacteria)、變形菌門(Proteobacteria)、綠彎菌門(Chloroflexi)和厚壁菌門(Firmicutes)為土壤中的優(yōu)勢菌門,分別占細菌總豐度的23.6%~45.1%、16.9%~28.4%、6.1%~19.0%和5.6%~13.8%(圖4(a)),這些優(yōu)勢菌門在其他研究中也有報道[7-8,46-47].與CK組相比,施肥組土壤中放線菌門的相對豐度下降,而變形菌門的相對豐度升高,這與已有研究結(jié)果一致[7,48].變形菌門屬于富營養(yǎng)型菌,施入土壤中的雞糞易分解[49-50],為該類菌的生長提供了豐富的營養(yǎng)物質(zhì),從而促進了它們的生長[51].與FLM組相比,稻殼還田增加了FLMS組中綠彎菌門和厚壁菌門的相對豐度,這與以前的研究結(jié)果一致[8,46].綠彎菌門和厚壁菌門是有機物分解的重要參與者[52],稻殼還田可改善土壤結(jié)構(gòu),增加土壤有機質(zhì)含量,提高養(yǎng)分利用率,從而促進這兩類菌的生長[53].
圖3 不同施肥處理土壤中ARGs亞型變化情況
選取相對豐度>0.1%的ARGs亞型和相對豐度前50%的MGEs
表2 不同施肥模式下土壤細菌Alpha多樣性指數(shù)
在屬水平上,相對豐度大于1.0%的微生物共檢出19種,占細菌總豐度的46.6%~57.2%.它們主要來自上述4類優(yōu)勢菌門、酸桿菌門(Acidobacteriota)和芽單胞菌門(Gemmatimonadota)(圖4(b)).其中,厚壁菌門中的芽孢桿菌屬()在各處理組中相對豐度最高(占3.55%~8.76%).與CK組相比,芽孢桿菌屬的相對豐度在施肥處理組中呈現(xiàn)不同程度的升高,FLMS組增幅最大為1.8倍,芽孢桿菌屬能很好的適應(yīng)環(huán)境條件,具有改善土壤養(yǎng)分狀態(tài)和促進植物生長的作用[54].
土壤中抗生素和ARGs的冗余分析結(jié)果見圖5,RDA1和RDA2兩軸共解釋了總變量的54.15%. TCs類抗生素是影響土壤中ARGs分布的主要因子,與四環(huán)素類ARGs、磺胺類ARGs以及MGEs正相關(guān),表明設(shè)施菜地土壤中TCs濃度升高,對ARGs造成選擇壓力[55],MGEs通過對抗性基因的捕獲、積累和擴散促進DNA在胞內(nèi)或胞外的移動性[56],增加水平轉(zhuǎn)移的風(fēng)險.此外,MLs類抗生素與MLS類抗性基因呈現(xiàn)相關(guān)性,抗生素的選擇壓力以及它們所引起的細菌群落變化可能是影響ARGs組成的驅(qū)動因素[55,57].
ARGs、MGEs和細菌群落的共現(xiàn)網(wǎng)絡(luò)關(guān)系見圖6,該圖由59個節(jié)點和117條邊構(gòu)成.ARGs與MGEs之間的共現(xiàn)意味著它們?nèi)菀自诃h(huán)境中轉(zhuǎn)移[37].例如,轉(zhuǎn)座酶基因A-04與Edelta1-01、G-02、F和D等8種ARGs正相關(guān),A-05與A1、G-02和A等6種ARGs正相關(guān);插入序列IS613與R、Edelta1-02和G-01等5種ARGs正相關(guān).這些結(jié)果表明MGEs可能促進多種ARGs在土壤中的擴散,從而增加了土壤的潛在生態(tài)風(fēng)險[58].
圖4 不同施肥模式下土壤細菌群落組成
圖5 設(shè)施菜地土壤中抗生素和ARGs的冗余分析
ARGs與細菌的顯著正相關(guān)關(guān)系可用于識別ARGs的潛在宿主[59].而當(dāng)ARGs宿主為病原菌時,其生態(tài)風(fēng)險應(yīng)引起優(yōu)先關(guān)注.例如,微枝形桿菌屬()與2、Edelta1-02和R基因等7種ARGs具有正相關(guān)關(guān)系,說明該菌可能是多種ARGs的潛在宿主[32].同時,也是一種致病菌[60],并且可能通過A-04實現(xiàn)ARGs水平轉(zhuǎn)移.芽孢桿菌)與A-02和C正相關(guān),而某些芽孢桿菌屬具有致病性[61].綜上可知,除抗生素的選擇壓力外,細菌和MGEs也是影響土壤中ARGs分布的重要因素[10,32,59].
圖6 ARGs、MGEs和細菌屬水平之間的共現(xiàn)網(wǎng)絡(luò)關(guān)系
選取平均相對豐度大于0.01%的ARGs、10種MGEs和平均相對豐度大于1%的細菌屬繪制,節(jié)點大小代表相對豐度大小.Spearman相關(guān)系數(shù)>0.8,<0.05
本文對土壤混合樣品的抗生素和ARGs進行了分析,有關(guān)不同處理組之間的差異有待進一步驗證.此外,本文在土壤-番茄系統(tǒng)中研究了不同施肥模式下土壤中抗生素和ARGs的變化情況,但未關(guān)注植物中抗生素和ARGs.植物微生物組是ARGs的重要儲庫,可通過食物鏈進人體內(nèi),產(chǎn)生抗生素耐藥問題,在未來研究中需重點關(guān)注.
3.1 設(shè)施菜地土壤中共檢出14種抗生素,施用有機肥增加了土壤中抗生素殘留,有機肥減量可有效降低抗生素污染,特別是TCs類.
3.2 設(shè)施菜地土壤中共檢出129種ARGs,單施有機肥組ARGs相對豐度最大,減量施用有機肥可降低ARGs種類和豐度,稻殼還田對ARGs的形成和傳播具有一定的阻控作用.
3.3 施用有機肥可增加土壤中微生物群落多樣性,秸稈還田提高了土壤有機質(zhì)含量,增加了綠彎菌門和厚壁菌門的豐度,促進芽孢桿菌屬的生長.
3.4 土壤中TCs類抗生素與四環(huán)素類抗性基因及MGEs正相關(guān),A-04A-05和IS613可能會促進ARGs的傳播,致病菌可能是ARGs的潛在宿主,增加ARGs的生態(tài)風(fēng)險.
3.5 設(shè)施蔬菜生產(chǎn)過程應(yīng)合理施肥,適當(dāng)減少糞肥的投入,增加作物回田以提高土壤養(yǎng)分含量.優(yōu)化有機肥生產(chǎn)工藝,削減糞肥中抗生素和抗性基因含量.
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Effects of fertilization regimes on antibiotics and antibiotic resistance genes in greenhouse soil.
LIU Xiao-ying1, LI Ying1, GENG Jia-gen1, WANG Jie1, CHEN Qing1, LI Si1,2*
(1.Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resource and Environmental Science, China Agricultural University, Beijing 100193, China;2.Yantai Institute of China Agricultural University, Yantai 264670, China)., 2023,43(2):772~780
In this study, the surface soil (0~20cm) under different fertilization regimes was collected from a vegetable greenhouse and 83 antibiotics and 203 antibiotic resistance genes (ARGs) were analyzed. The results showed that a total of 14 antibiotics, 129 ARGs subtypes and 10 mobile genetic elements (MGEs) were detected in the soil. Tetracyclines (TCs) were the dominant antibiotics in soil, and β-lactams and multi-drug resistance genes were the dominant ARG types. Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes were the main bacterial phyla in soil under different treatments. Fertilization increased the diversity and abundance of antibiotic residues and ARGs in soil, and increased the-diversity of soil bacterial communities. The relative abundances of antibiotics, ARGs and MGEs were the highest in the treatments of manure alone and manure plus chemical fertilizer, and they were decreased by applying reduced manure. The return of rice husk to the field was helpful in controlling the pollution of antibiotics and ARGs. The selection pressure from antibiotics, changes in bacteria community and MGEs were the driving factors affecting the distribution of ARGs in greenhouse vegetable soil.
antibiotics;antibiotic resistance genes;antibiotic resistance mechanism;microbial diversity;greenhouse soil
X53
A
1000-6923(2023)02-0772-09
劉肖應(yīng)(1997-),女,四川自貢人,中國農(nóng)業(yè)大學(xué)碩士研究生,從事新污染物治理研究.
2022-06-07
山東省自然科學(xué)基金資助項目(ZR2020QD132);北京高校卓越青年科學(xué)家計劃項目(BJJWZYJH01201910004016)
* 責(zé)任作者, 副教授, sili@cau.edu.cn