Bacterial and Archaeal Diversity in Sediments of West Lake Bonney

Published Ahead of Print 26 November 2012. 10.1128/AEM.02336-12. 2013, 79(3):1034. DOI:

Appl. Environ. Microbiol. Chao Tang, Michael T. Madigan and Brian Lanoil Dry Valleys, Antarctica Sediments of West Lake Bonney, McMurdo Bacterial and Archaeal Diversity in /content/79/3/1034Updated information and services can be found at: These include:

SUPPLEMENTAL MATERIAL

Supplemental material REFERENCES /content/79/3/1034#ref-list-1

This article cites 6 articles, 0 of which can be accessed free at: CONTENT ALERTS

more»articles cite this article), Receive: RSS Feeds, eTOCs, free email alerts (when new /site/misc/reprints.xhtml Information about commercial reprint orders: /site/subscriptions/

To subscribe to to another ASM Journal go to: on May 6, 2014 by Nanjing University

/Downloaded from

Bacterial and Archaeal Diversity in Sediments of West Lake Bonney, McMurdo Dry Valleys,Antarctica

Chao Tang,a*Michael T.Madigan,b Brian Lanoil a*

Department of Environmental Sciences,University of California,Riverside,California,USA a;Department of Microbiology,Southern Illinois University,Carbondale,Illinois, USA b

Bacterial and archaeal diversity was examined in a sediment core from Lake Bonney,Antarctica.Members of the Archaea showed both low abundance and diversity,whereas bacterial diversity was moderately high and some phyla were fairly abun-dant,even in geologically old samples.Microbial diversity correlated with sample texture and differed in silty and coarse samples.

S everal permanently ice-covered lakes exist in the McMurdo Dry Valleys,Antarctica(MCM),with ice covers ranging from 3to6m.The limnological properties of MCM lakes can vary dramatically from lake to lake and are likely a response to local geochemical and climatic factors over time(1,2).Wind mixing and other major currents do not exist in these lakes,and sedimen-tation is primarily due to aeolian dust,soil,and weathered rocks that blow onto the ice cover and are transported through the ice to the sediments(3).Benthic microbial mats stabilize and colonize MCM lake sediments(4),and repeated cycles of microbial mat growth and burial by deposition are thus the main sediment-forming mechanisms(3,4).This process is very slow;estimates of sediment accumulation from sediment traps show a rate of just 0.02to0.9mm yearϪ1(3),and sediments are well preserved on time scales of thousands of years(5).

We have examined microbial diversity in the sediments of west Lake Bonney(WLB),located in the Ta

ylor Valley.From a nearly 4-m core of WLB sediments,we sampledﬁve sections(Table1); DNA was extracted from each,and16S rRNA genes were resolved by denaturing gradient gel electrophoresis(DGGE)and/or clone library construction(see the supplemental material).

DGGE analyses of16S rRNA gene products from members of the Bacteria yielded46bands(Fig.1A).The banding patterns in sections5I,5II,and4I were very similar,while section4II yielded the most distinct pattern(Fig.1A).Major phylotypes included the Bacteriodetes(22bands)and the Proteobacteria(10total bands, with4members of the Alphaproteobacteria,1of the Betaproteo-bacteria,and5of the Gammaproteobacteria).Other phyla in-cluded the Firmicutes(5bands),the Actinobacteria(3bands),and one member of the Acidobacteria.Archaeal DGGE proﬁles showed very few bands(Fig.1B),all of which associated with members of the Thaumarchaeota and the Crenarchaeota from various environ-ments;these likely originated with sediment deposition.The as-semblages of the Archaea were indistinguishable except for sample 4II.Only one archaeal phylotype was found previously in the Lake Bonney water column,and it was associated with the Euryar-chaeota(6).Thus,the water column and the sediments appear to support different phyla of the Archaea.

Individual clone libraries for the Bacteria were constructed for all samples except5II.The four libraries

contained a total of442 clones(175operation taxonomic units[OTUs][Table1]).Partial 16S rRNA gene sequences were obtained for290clones;section4I yielded137clones,4II yielded68clones,5I yielded63clones,and 5III yielded22clones.Both the Shannon diversity index(SDI)and Chao-1analysis showed moderately high bacterial diversities in all Received

25July2012Accepted16November2012

Published ahead of print26November2012

Address correspondence to Brian Lanoil,brian.lanoil@ualberta.ca.

*Present address:Chao Tang,BioMerieux(Shanghai)Company Limited,Pudong,

Shanghai,China;Brian Lanoil,Department of Biological Sciences,University of

Alberta,Edmonton,Alberta,Canada.

Supplemental material for this article may be found at /10.1128

/AEM.02336-12.

doi:10.1128/AEM.02336-12

TABLE1Sample characteristics of a4-m WLB sediment core and clone library analyses for members of the Bacteria

Section Depth(cm)Texture description Composition No.of

clones

No.of

OTUs

dmx512协议Chao-1value with95%

conﬁdence interval a

Good’s

coverage(%)SDI

4I5–10Intermediate dryness with silt/

sand,few pebbles Mixture of microbial mat and

terrigenous materials

188111272(194,421)60.6 4.5

4II50–55Solid,large clasts,sand/soil-like Mainly terrigenous particles10660129(89,222)63.2 3.9 5I150–155Very moist,ﬁne-grained

material

Microbial mat10653110(75,197)69.8 3.7

5II250–255Larger clasts with someﬁne-

grained material Mixture of microbial mat and terrigenous materials

5III350–355Large dry clasts,coarse material Mainly terrigenous particles422278(35,272)64.3 2.8

Total442175383(294,538)76.9 4.7 a Chao-195%conﬁdence interval lower bound and Chao-195%conﬁdence interval upper bound are shown in parentheses following Chao-1richness estimation.

Applied and Environmental Microbiology p.1034–1038February2013Volume79Number3 on May 6, 2014 by Nanjing University / Downloaded from

sediment sections(Table1).Good’s coverage varied from60%to 70%,suggesting that cloning captured the dominant phylotypes. Both Chao-1and SDI values decreased with depth,while Good’s value increased(except in section5III)(Table1),signaling a general decrease in bacterial diversity with increasing depth in the sediment.

The Bacteroidetes and the Proteobacteria were the dominant phyla(ϳ36and38%,respectively)(Fig.2).Low-abundance phyla included the Planctomycetes(5.2%)and the Verrucomicrobia (4.3%);TM7,the Chloroﬂexi,WYO,and the Lentisphaerae had two or fewer clones each(Fig.2).The bacterial assemblage in core section5III was clearly distinct from those in the other sections, and each section contained several unique OTUs:4I,50%;4II and 5I,25%each;and5III,57%.The software program TreeClimber indicated that the assemblages in sections4I and5I were not sig-

FIG1UPGMA cluster analysis of the bacterial and archaeal community structure in each WLB core section based on the DGGE banding patterns and OTU distribution of bacterial clone libraries.Dice similarity coefﬁcients of bacterial DGGE banding patterns(A)or archaeal DGGE banding patterns(B)are shown.“N”in front of the gel label indicates nested PCR.Note that sample5III did not yield a PCR product for the Archaea .

FIG2Distribution of bacterial phyla in each individual clone library.The y axis represents each(sub)phylum’s clone coverage of each section’s clone library. Low-abundance phyla not shown included the Acidobacteria(3clones;section4I had2singlets,and section5I had1singlet),candidate division TM7(section 4I had2singlets),the Chloroﬂexi(section4I had1singlet),candidate division WYO(section5I had1singlet),and the Lentisphaerae(section5III had1singlet).

Microbial Diversity in WLB 1035 on May 6, 2014 by Nanjing University / Downloaded from

niﬁcantly different from each other but that the assemblage in4II was distinct(see Table S3in the supplemental material).More-over,the͐-LIBSHUFF software program indicated that clones from4II and5I could be subsets of4I but those from sections4II and5I were distinct(see Table S3).破窗器

About50%of the WLB sediment clones grouped in OTUs having at leastﬁve representatives(“major OTUs”).Many of these clustered within clades that contained phylotypes identiﬁed in Antarctic or other constantly cold environments(Fig.3;see also Fig.S1in the supplemental material).Three major OTUs(OTU 127and OTU140of the Gammaproteobacteria and OTU44of the Planctomycetes)were closely related to phylotypes from the WLB water column(6).Except for members of the Firmicutes related to halophilic phylotypes(see Fig.S1),the remaining major OTUs were related to phylotypes identiﬁed in diverse environments and are likely derived from external sources.

Bacterial diversity was higher in WLB sediments than in the water column.Major bacterial phyla detected in sediments in-cluded all of the phyla detected in Lake Bonney water,such as the Bacteriodetes and the Proteobacteria(6),plus several minor phyla. The moderately high bacterial diversity found even in old sedi-ment sections underscores the similarity of WLB sediments to stromatolites in preserving a record of prokaryotic diversity.The ﬁve sections of the core were of different textures,indicating dif-ferent sources of sedimentary material.Theﬁne,silty layers were likely derived from relic microbial mats.Phylotypes retrieved from

0.10

5I.125 (JX948451)(OTU81,15)

Flavobacterium sp. WB4.3-19 (hard water creek, AM177629)

Flavobacterium sp. WB 3.4.10 (hard water creek, AM177622)

Flavobact erium pect inovorum(AM230490)

Glacier bacterium FJS20 (Southern Alps of New Zealand, AY315160)

JEG.g1 (John Evans Glacier, DQ228408)

4I.9D (JX948452)(OTU31,6)

Antarctic bacterium R-7933 (Lake Fryxell mat, AJ440987)

Flavobacterium sp. WB4.2-37 (hard water creek, AM934668)

Flavobact erium johnsoniae(AM921621)

Antarctic bacterium R-7550 (Lake Fryxell mat, AJ440979)

Flavobact erium psychrolimnae(AJ585428)

JEG.f1 (John Evans Glacier, DQ228406)

Flavobacterium sp. ER3 (Antarctica soil, FJ517631)

Flavobacterium sp. BSs20191 (DQ514307)

4I.23 (JX948453)(OTU5,5)

Flavobact erium degerlachei(AB455258)

汽车软管

100

4II.6D (JX948454)(OTU86,8)

Flavobact erium gelidilacus(EU090722)

Antarctic bacterium R-9033 (Ace Lake mat, AJ441001)

Flavobact erium kamogawaensis(AB275999)

ARKICE-35 (Arctic sea ice, AF468305)

ARKXV/1-43 (Arctic pack ice, AY165589)

ARKXV/1-145 (Arctic pack ice, AY165588)

Gillisia mitskevichiae(AY576655)

5I.1 (JX948455)(OTU28,10)

Flavobacteriaceae bacterium ACEMC 7-3 (FM163099)

100

Gillisia sp. ZS4-6 (FJ889670)

Gillisia limnaea(AJ440991)

4I.75 (JX948456) (OTU43,9)

Sc8 (hydrocarbon polluted sand, EU375196)

Gelidibacter sp. ZS2-2 (Antarctic Ocean, FJ196005)

Subsaxibact er broadyi(AY693999)

72自动排污阀

Antarctic bacterium R-9217 (Ace lake mat, AJ441008)

Gelidibacter algens(AF001367)

100

Roi_L1-G12-T7(Lake Roi, FN296934)

SF54(mesotrophic lake Schöhsee, AJ697701)

5I.44 (JX948457)(OTU15,11)

FNE11-34 (Lake Grosse Fuchskuhle, DQ501310)

Fluviicola taffensis(AF493694)

HTCC4118 (McMurdo Dry Valley lake, EF628495)

HTCC4126 (McMurdo Dry Valley lake, EF628500)

4I.12C (JX948458)(OTU20,9)

4II.6B (JX948459)(OTU6,9)

ARCTIC47_D_06 (Arctic, EU795246)

Algoriphagus sp. ZS3-3 (Antarctic ocean, FJ196000)

Algoriphagus ant arct icus(AJ577142)

Algoriphagus yeomjeoni(AY699795)

Algoriphagus rat kowskyi(U85891)

Flectobacillus sp. HTCC553 (Crater Lake, AY584584)

Granotes_C-G12-907R (Lake Granotes, FN297694)

4II.25 (JX948460)(OTU122,5)

glb292b (glacier ice, EU978780)

溴代环丙烷92

Arcicella sp. AKB-2008-JO107 (lake water, AM988937)

Arcicella rosea(GU368373)

100

FIG3Phylogenetic analysis of major OTUs of the Bacteroidetes(A)or the Proteobacteria(B)from the WLB sediment core.Bolded sequences are from this study; one representative clone from each major OTU is shown,and in the following parentheses,the OTU name and the number of clones belonging to this particular out,separated by a comma,are listed.Both trees were rooted with Bacillus

subtilis(D26185)and constructed by maximum likelihood.A mask of702(A)or691 (B)nucleotides with nonambiguously aligned positions was used.Bootstrap values(100replicates)above60are shown above relevant nodes.GenBank accession numbers of sequences from other studies are included.

Tang et al.

Applied and Environmental Microbiology on May 6, 2014 by Nanjing University / Downloaded from

such samples were closely related even though they were physically separated in the core and thus were of different ages.This may reﬂect the unique composition of microbial mats and underscores the fact that diversity can be preserved over long time periods.

The sandy and clastic layers probably contained more terrige-nous materials from episodic depositions of particles blown in from the surrounding hills.We hypothesize that under different climatic conditions,the terrigenous materials that form the clastic samples are probably associated with different bacterial commu-nities.Thus,silty samples would be useful for testing the evolution of microbial mats in MCM lakes,while clastic samples might be useful for examining the effect of climatic conditions on MCM microbial communities.

In summary,WLB sediments appear to be composed of both stromatolite-like mat-derived materials,with their layered struc-ture and long-term record of microbial diversity,and rougher, more clastic materials.Prokaryotic diversity inﬁne-grained WLB sediment layers varied less with depth than did layers consisting of primarily clastic terrigenous materials.The microbial diversity of the coarse layers may therefore be a better record of climatic im-pacts and wind-blown materials than are theﬁne-grained sedi-ments.We conclude that differences in prokaryotic community

0.10

4II.35 (JX948461)(OTU125,19)

glb262b (glacier ice, EU978750)

JEG.e1 (John Evans Glacier, DQ228403)

ANTLV7_H07 (Lake Vida ice cover, DQ521547)

JFJ-ICE-Bact-06 (melted-ice water, AJ867749)

Polaromonas ginsengisoli(AB245355)

4I.79 (JX948462)(OTU21,7)

AK1AB1_08C (soil, GQ396835)

SIB2 4D (subglacial, DQ628931)

Elb24 (Elbe river, AJ421913)

Rhodoferax ferrireducens(AF435948)

100

4II.5B (JX948463)(OTU101,10)

Arctic_23 (Arctic, EF379215)

KD1-44 (penguin droppings sediments, AY218562)

ZWB4-12 (Zoige Alpine Wetland, FJ801209)

Hydrogenophaga t aeniospiralis(AF078768)

100

Antarctic bacterium R-8890 (Ace Lake mat, AJ440995)

B8_11 (PAH-contaminated soil, FJ184322)

St enot rophomonas rhizophila(GU391467)

4II.29 (JX948464)(OTU95,6)

100

Marinobacter sp. BF04_CF-4 (Blood Falls, DQ677876)

WLB16-007 (West Lake Bonney, DQ015849)

5III.12 (JX948465)(OTU127,9)

ELB25-092 (East Lake Bonney, DQ15769)

Marinobacter sp. ELB17 (East Lake Bonney, AY518678)

Marinobacter sp. ANT8277 (Antarctic pack ice, AY167267)

ANTLV_A07 (Lake Vida ice cover, DQ521533)

Marinobact er sediminum(AJ609270)

100

Pseudomonas fulva(AM411071)

Pseudomonas parafulva(AB060133)

4II.31 (JX948466)(OTU104,11)

100

VHS-B1-16 (harbor sediment, DQ394897)

WLB13-127 (West Lake Bonney, DQ015840)

5I.98 (JX948467)(OTU140,9)

ELB25-204 (East Lake Bonney, DQ015838)

100

Escherichia coli(J01695)

4I.12H (JX948468)(OTU22,5)

FGL7S_B135 (Green Lake sediments, FJ437932)

Agrobact erium sanguineum(AB062106)

Antarctic bacterium R-9478 (Ace Lake mat, AJ441013)

5I.35 (JX948469)(OTU51,5)

1C226554 (Newport Harbour, EU799003)

XZXXH49 (high-altitude freshwater, EU703439)

Sphingomonas sp. UF010 (AB426571)

100

5m-88 (Y ellow Sea, GU061259)

ctg_CGO F113 (deep-sea octacoral, DQ395777)

粉尘气溶胶发生器

4II.32 (JX948470)(OTU97,5)

S3-11 (marine water, EF491395)

Lokt anella salsilacus(AY771761)

WLB13-220 (West Lake Bonney, DQ015846)

100

Paracoccus denitrificans(X69159)

100

5I.32 (JX948471)(OTU73,6)

XZQH56 (high-altitude polysaline lake, EU703271) Orientia tsutsugamushi(D38627)

100

FeO rig_B_136 (methane seep sediment, GQ357040)

BC_B2_4b (Eel River Basin, EU622296)

5III.61 (JX948472)(OTU155,7)

Desulfobact erium anilini(AJ237601)

100

Desulfobact er vibrioformis(U12254)

100

Desulfovibrio desulfuricans(AF192153)

83 77βγαδ

FIG3(Continued)

Microbial Diversity in WLB 1037 on May 6, 2014 by Nanjing University / Downloaded from

本文发布于:2024-09-23 00:33:08，感谢您对本站的认可！

本文链接：https://www.17tex.com/tex/4/190845.html

上一篇：生物分类总表

下一篇：湖泊沉积物中微生物与生物地球化学循环

标签：软管自动粉尘汽车排污阀气溶胶

留言与评论（共有 0 条评论）