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Diversity of Polar Monothalamous Foraminifera –

Morphological and Molecular Approach

Anna Sabbatini

Department of Marine Sciences, Polytechnic University of Marche,Via Brecce Bianche, 60131, Ancona, Italy

Introduction

In many marine areas, Foraminifera are a dominant meiofaunal group in terms of both numerical

abundance and biomass. Monothalamous (single-chambered) species with either agglutinated or

organic-walled shells (‘allogromiids’ in the broad sense) are an important component of marine

foraminiferal assemblages, particularly in fine-grained sediments, for example in the deep sea and in

high latitudes regions (Gooday, 2002). Monothalamous Foraminifera also occur in freshwater

environment (Holzmann et al. 2002, 2003) and have even been discovered to live in a damp terrestrial

habitat (Meisterfeld et al. 2001). These delicate Foraminifera often account for 10-20% of individualsand species in deep-sea samples (Gooday, 2002). In Polar coastal regions, influenced by turbid glacial

melt water, and in some estuaries, allogromiids (including saccamminids) represent an even higher

proportion of live Foraminifera, in some cases >90% (Gooday, 2002).

Despite of their high abundance and ecological importance, the diversity of monothalamous

Foraminifera is very poorly known. Relatively few species have been described and most of these come

from easily accessible, intertidal environments. Deeper sea samples routinely yield ten or more

undescribed species (Gooday et al. 1998). Several new morphotypes of allogromiids have also been

reported from Antarctic coastal waters (Gooday et al. 1996). Several new species of polar and subpolar

monothalamous Foraminifera have been described (Gooday et al. 1995; DeLaca et al. 2002; Wilding2002) or redescribed (Bowser et al. 2002) during the past few years. Because the morphological

characters are not always sufficient to establish the phylogenetic relationships among allogromiids,

many recent species descriptions include the analysis of molecular data (Pawlowski et al. 2002a;

Cedhagen and Pawlowski, 2002; Gooday et al. in press; Gooday and Pawlowski, submitted; Sabbatini

et al., 2004).

Molecular phylogenetic studies challenged the traditional, morphology-based classification of

Foraminifera, prompting a profound revision of higher-level taxonomy and species identification

(Pawlowski 2000, Pawlowski and Holzmann 2002). Phylogenetic analysis of molecular data, based

mainly the small subunit ribosomal RNA and actin gene sequences, revealed that the Foraminifera

include not only testate marine species but also the naked freshwater amoeboid protists (Pawlowski et

al. 1999). Molecular studies also show that there is no clear boundary between allogromiids in the

‘traditional’ sense (i.e. organic-walled species) and single-chambered agglutinated Foraminifera,

traditionally considered as astrorhizids, suggesting that all of them form a paraphyletic group of

monothalamous Foraminifera (Pawlowski et al., 2002a, 2003). A particularly high taxonomic diversity



of allogromiid Foraminifera, represented in majority by undescribed species, was revealed by molecular

study of Antarctic Foraminifera (Pawlowski et al. 2002b).

At the beginning of project the main objective was to describe new Antarctic monothalamous

Foraminifera. Many of these Foraminifera were isolated and molecularly characterized in preceding

study (Pawlowski et al. 2002c) but could not be attributed to any known species. During the year there

was possibility to collect other samples but in a different site and environment (Porcupine Abyssal

Plain, NE Atlantic Ocean). The morphological analyses carried out on board on superficial sediment

samples revealed an interesting monothalamous foraminiferal fauna composed especially by specimens

belonging to Komokiacea group. These specimens are really poor known and the most recent studies

are by Schroder et al. (1989), Gooday (1982, 1983), Gooday & Cook (1984), Tendal (1972, 1979),

Tendal & Hessler (1977), Kamenskaya (1990, 1993).

Since there are no sequences available of Komokiacea yet, and several samples of them were available

also from Antarctica to study, new aim was describe and identify a larger number of komokiacean

specimens from these two sites and where possible correlate them. Important goals are 1) molecular

data of Komokiacea group from the Atlantic Ocean in order to reveal them taxonomic diversity and

phylogenetic position within the Foraminifera 2) a comparison of species present in the Antarctic and

NE-Atlantic areas of study 3) morphological description of new species. I focused on the above points

1 and 2.

Komokiacea (Textulariina, Foraminiferida, Protista) are agglutinated Foraminifera with test consisting

of a complex system of fine, branching tubules of even diameter. The test wall is simple, with

argillaceous particles. Stercomata accumulate within the tubules. The group has worldwide distribution,

particularly in the abyssal zone. The greatest relative abundances have been found in abyssal

oligotrophic areas and in hadal trenches. Tendal & Hessler (1977) divided Superfamily Komokiaceain two families Komokiidae (Tendal & Hessler, 1977) and Bacullelidae (Tendal & Hessler, 1977). First

have test bushy or arborescent constructing widely spaced branching cylindrical tubules and second test

variously shaped, sparsely branched or dense clump. Branching is the basic feature controlling body

form. In most cases branching is dichotomous, although tri- or polychotomy also exists. In the tube wall

two layers can be distinguished: the inner layer is generally very thin and frequently laminated while

the outer part is composed by agglutinated sediment. Komokiacea are devoid of real apertures. The

pseudopodia must penetrate the tube wall through minute pores having possibly temporary character

(Tendal & Hessler, 1977). The Komokiacea vary in according to the amount and type of particles in the

agglutinated layer.

Material and Methods

Specimen collection

The material for this study was collected in the Weddel Sea (Antartica) during R/V Polarstern cruise

ANT-XIX/4 (ANDEEP II, February 28th to April 1st, 2002) (Figure 1).



The other material was collected in the Porcupine Abyssal Plain (NE – Atlantic Ocean) in June 2004

(Figure 2). The Foraminifera (not only Komokiacea for a total of 80 samples) for molecular work have

been isolated and stored in guanidine. Sediment samples for morphological studies were sieved on 300

micron mesh and preserved in formalin 10%. All monothalamous soft-walled Foraminifera (organic

and agglutinated) will be sorted by hand, under a stereoscopic microscope, from the floated residue.

Individuals will be placed in glycerol on a cavity slide, described, photographed and classified.

DNA extraction, amplification and sequencing

DNA was extracted from single or several cells using the guanidine method as described in Tkach

& Pawlowski (1999). PCR amplifications were performed in a total volume of 50 l with an

amplification profile consisting of 40 cycles of 30s at 94C, 30s at 48C and 120s at 72C, followed by

5 min at 72C for final extension. A fragment of the SSU rRNA gene was amplified by PCR with the

primer pair s14F3 (5’ACG CA(AC) GTG TGA AAC TTG) and sB (5’ TGA TCC TTC TGC AGG TTC

ACC TAC). When the first PCR was unsuccessful, the PCR products were re-amplified using the nested

primer s14F1 (5' AAG GGC ACC ACA AGA ACG C), with an amplification profile consisting of 25

cycles and 52C for annealing time. A second series of analyses were carried out using the primer pair

s14F3 (5’ACG CA(AC) GTG TGA AAC TTG) and s17 (5’CGG TCA CGT TCG TTG C) for the PCR

and the same nested primer (5' AAG GGC ACC ACA AGA ACG C) for the re-amplification. The

amplified PCR products were purified using High Pure PCR Purification Kit (Roche Diagnostics), then

either sequenced directly or ligated into pGEM-T Vector system (Promega) and cloned in XL-2

Ultracompetent Cells (Stratagene). Sequencing reactions were prepared by using ABI-PRISM Big Dye

Terminator Cycle Sequencing Kit and analysed with an ABI 3100 DNA sequencer (Perkin-Elmer), all

according to the manufacturer’s instructions.

Sequence analysis

Sequences were aligned manually to the large database of foraminiferal sequences, using theSeaview software of Galtier et al. (1996) and Bioedit program (2004). A fragment of 462 sites was used

for the analysis with sB primer and a fragment of 100 sites was used for analysis with s17 primer.

Phylogenetic analyses were performed with the neighbor joining method (NJ) using Kimura 2 distance

algorithm.

Result Morphological work

Here I present a short taxonomic survey of some of the must abundant larger (>300 micron) rhizopod

species, representing a wide range of taxa, from populations on both the Porcupine Abyssal Plain and

Weddel Sea.The species and morphotypes from both study sites were divided into taxonomic categories in most

cases genera such as Ipoa spp., Komokia spp., Lana spp., Normanina spp. and Septuma spp. but also

indeterminate groups, e.g. Chain spp.

“Chain-like” komokiaceans:

These are common in the Porcupine Abyssal Plain and it is possible distinguish 7 morphotypes. The

“chains” often consist of a branched or occasionally branching chain of small spherical chambers



connected by long, narrow, gently tapering necks. Occasionally globigerinacean tests of varying size

are incorporated within the chamber wall. Other types are organized as a rigid chain of irregularly-

shaped, elongate chambers connected by narrow necks. The chambers are angular; long narrow tubules

of even width may extend from the end of the chamber. The test wall consists of globigerinacean tests

of variable size. Similar morphotypes are distinguished from these forms by the irregularly-shaped

chambers as well as by chambers separated by rigid, short, narrow necks. Other “Chain-like” forms

consist of a series of spherical/ cylindrical chambers which adjoin directly; the chambers have a bumpy

exterior surface, incorporating globicerinacean tests of varying size incorporated. Occasional long,

single filaments may extend from the surface. Sometimes irregularly shaped chains of chambers are

densely encrusted with globicerinacean tests which obscure the basically organic test wall and make

individual chambers difficult to distinguish. Also in this case occasional short, fine, transparent fibres,

and long, white filaments, extend from the surface. In other species, a branching chain of triangular,

claw or arrow-head shaped chambers joined together at their pointed ends to produce a chain with an

elegant appearance. Finally, a distinctive morphotype comprises pear-shaped chambers joined to form

a branching chain which undergoes characteristic angular changes of direction. The chambers are joined

head-to-toe (Plate 1).

All chain-like morphotypes are quite delicate, they break easily and are typically found in a fragment

state.

Komokia-like group

This group is dominant in samples from Porcupine Abyssal Plain area; some specimens Komoki-like

were found also in the Antarctic study area.

According to Tendal & Hessler (1977), Komokia morphotypes have generally bush –like body

consisting of mostly dichotomously branching tubules without anastomoses, the branching points

occurring at any place along the tubules. Ramification increases toward periphery of body. All tubulesare the same diameter (more less), and are nonseptate (Tendal & Hessler, 1977).

In our material the interstices between the tubules are sometimes filled with abundant sediment and the

general body form is elongate, pear or club-shaped body. Long, umbranched, empty filaments of

varying length, frequently extend from the surface. Specimens often differ from classical representatives

of the genus is consisting of only a few tubules. Globigerinacean tests are occasionally attached to

branching tubules (Plate 2).

Genus Lana and Reticulum

Species of the closely-related genera Lana are common in both study areas. Lana species have the formof a loose mass of branching and anastomosing tubules with no centre of organization or pattern of

growth. The tubules are parallel sided and non-septate (Tendal & Hessler, 1977). In Reticulum the

tubules anastomose more extensively to than in the case of Lana. It is possible to recognize a large

number of morphotypes and classification is based on form of the clump, on the frequency of

anastomoses, and on the degree of filling of interstices with sediments (Gooday & Cook, 1984).

The species of Lana and Reticulum studied vary from irregularly-shaped clump of fine, or very fine,



branching and anastomosing tubules of even diameter to a pear-shaped, tightly packed clump of tubules

of even diameter. There are also morphotypes represented by coherent, spongy, irregularly to

spherically-shaped masses of regularly anastomosing tubules or loose network of branching tubules

(sometimes fine) anastomosing, and not always of even diameter. The interstices of the Lana/Reticulum

tubule system are either devoid of sediment or sediment-filled; the tubules may be transparent and

tipically contain dark masses of stercomata. Globigerinacean tests are often incorporated within the

tubules network or throughout tubule clump (Plate 3).

Ipoa group

Morphotypes belonging to Ipoa group are better represented in the Antarctic environment.

Most specimens are tree-like fragments treelike with a basal stem followed by burst of tightly spaced

multiple branching; diameter of tubules decreases with each branching. Tubules are avoid of septa

(Tendal & Hessler, 1977) (Plate 4).

Normanina group

Also specimens belonging to this group are also more common in the Antarctic although there are some

PAP representatives.

They have a base or center composed of tubules branching in complex, irregular pattern. Tubules radiate

outward from this base and terminate in globular or clublike chambers (Tendal & Hessler, 1977) (Plate

4).

Septuma group

Species of Septuma group in the Antarctic samples are represented by specimens with bushlike body,

sparse branching, dichotomous and nonastomosing at base. All tubules, as suggested by the group name,

are divided internally by septa with foramina (Tendal & Hessler, 1977) (Plate 4).

Edgertonia spp. and Komoki mudball spp. these are the dominant benthic Foraminifera in the Porcupine

Abyssal Plain samples. In addition to the above mentioned Komokiacea, a number of other

monothalamous Foraminifera (Muddy Tube spp., Lagenammina spp., Rhizammina spp.) and

polythalamous (Reophax spp.) Foraminifera were studied in the Antarctic samples.

Result Molecular work

Sixty-seven samples from Porcupine Abyssal Plain (NE Atlantic Ocean) and 24 samples from Weddel

Sea (Antarctica) were analysed using molecular approach. It was possible obtain only DNA sequencesfrom fragment of the SSU rRNA gene of monothalamous agglutinated Foraminifera (Astrorhiizina) and

polithalamous agglutinated and calcareous Foraminifera (Textulariina and Rotaliina). Only 7 DNA

sequences from komokiacean morphotypes were obtained and results are represented in figure 3 (a-b).

We obtained also DNA sequences of monothalamous and polithalamous agglutinated Foraminfera

(Lagenammina spp., Reophax spp. and Rhizammina spp.) from the PAP; this is an important goal

because all data of this genera come from shallow water or polar settings. In this case we have the first



DNA sequences from deep Atlantic Ocean.

Discussion and Conclusion

Komokiacea are an important group of macrofaunal sized agglutinated Foraminifera. This group

of protists eluded, until recently, description because fragility of many species means that they were

often lost during sample processing or their identification and classification were difficult. Even when

present in sample residues, they are difficult to recognize as organisms (Tendal, 1979), looking instead

like non descript organic detritus, poorly washed balls of sediment, or minor fragments from the surface

of some unidentified larger organisms (Tendal & Hessler, 1977) (Gooday & Cook, 1984).

Very few observations have been made on live cells of Komokiacea although they are classified

within the Foraminifera, granulo-reticulate pseudopodia have not been observed in any true

komokiacean organisms, causing some workers to doubt their assignment to this group. The group has

non clear ultrastructural identity and is distinguished by the unusual gross morphology consisting of a

system of branching of tubules.

Usually foraminiferal species are identified exclusively on the basis of morphological characters,

such as the number and form of the chambers, the form of test periphery and the type of ornament.

However, the paucity of morphological characters and their relatively large variability renders species

identification in Foraminifera and in Komokiacea particularly difficult. In this project we therefore

made the first attempts to investigate what Komokiacea are and their phylogenetic position between

Foraminifera group based on molecular data. Our results are based principally on analysis of ribosomal

DNA sequences.

During the course of this project we met problems with PCR analyses and on primers use. PCR

is a tool of unrivalled power, but as is so often the case, this power is linked to unrivalled complexity.

The source of this complexity is the PCR reaction itself-a myriad of ionic interactions, kinetic constants,and enzymatic activities, all taking place repeatedly and, hopefully, perfectly, within the space of a few

hours. Because each DNA (template) and each primer pair is different, and because molecular

systematics tend to use a wide variety of taxa or primers in a single research program, PCR reactions

need to be carefully optimised. This means that a certain amount of trial and error is an integral part of

the PCR experience. Apart from PCR conditions attention has been focused on the primers and how

strongly they anneal to the template DNA. A first series of analyses have been made using foraminiferal

primers and in particular primers with monothalamous foraminiferal “target”. We obtained few results

associated to specimens belonging to polythalamous agglutinated (Reophax) and calcareous

(Epistominella) Foraminifera. A second series of analyses were made using universal eukaryotic primers obtaining only contaminant sequences of animal and fungi. Other studies will be made using

other foraminiferal primers. There is no evidence yet, but the possibility exists that these results could

lead us to not consider Komokiacea as Foraminifera.

On the other hand morphological features, wall composition and test structure all suggest that

Komokiacea are Foraminifera.

The test of Komokiacea are partially formed organically but it also include a varying proportion



of extraneous matter as the typical foraminiferal agglutinated tests. The foreign particles utilized in test

construction could reflect to some extent the local environment; material commonly utilized includes

quarts grains, various heavy minerals, clay or carbonate fragments or grains, and organic debris,

including tests of smaller Foraminifera, radiolarians, coccoliths, fragments of molluscan shells, and

sponge spicules (Loeblich & Tappan, 1964). However Komokiacea are known to accumulate very fine

particles within tubule lumen where they are presumably digested (Gooday & Cook,1984). Many

aspects of the ecology and biology of the Komokiacea are poorly understood: protoplasmic body,

nucleus, pseudopodia, gamets, cysts and in particular symbionts and parasites life history and feeding

habits are still unknown.

Little is known also about the distribution of komokiacean species (Schroder et al., 1989; Gooday

& Cook, 1984; Kamenskaya, 1993).

Systematic tree obtained from molecular data (figure 3) revealed the distribution of several

“komokiacean DNA sequences” with environmental DNA sequences or “not common foraminiferal

DNA sequences” in a clade of monothalamous agglutinated Foraminifera from several habitats. These

DNA sequences could belong to parasite organisms living in the sediment particles agglutinated by

Komokiacea. This strategy is common to several protozoans and from the literature we know that the

coccidian Trophosphaera planorbulinae (LE CALVEZ) (Loeblich and Tappan, 1964) lives in the larger

chambers of Elphidium crispum extending throughout the test and destroying it eventually. Nematode

worms may also be parasitic on them. An other condition is represented by bryozoan colonies that inter

grow as networks with the komokiacean tubules (Lana and Edgertonia genera) (Gooday & Cook, 1984)

forming a symbiotic relation between ctenostome peristomes of Bryozoa and the tubule mass of

Komokiacea. These kinds of relationships complicate the study of komokiacean molecular

identification.

Our findings suggest the following conclusions 1) to find DNA sequences of Komokiacea isnecessary perform the PCR analyses with new foraminiferal primers or other universal primers; 2) we

need to improve our knowledge of ultrastructural morphology in order to demonstrate that Komokiacea

are really Foraminifera; 3) we need more information about the natural history of Komokiacea in

general.

Figure Captions

Fig. 1 – Location Map Antarctic Samples

Fig. 2 – Location Map NE Atlantic Samples

Fig. 3 – Molecular data a) 462 sites were used for the analysis with sB primer; phylogenetic

analyses were performed with the neighbor joining method (NJ) using Kimura 2 distance algorithm;

b) 100 sites were used for analysis with s17 primer; phylogenetic analyses were performed with the

neighbor joining method (NJ) using Kimura 2 distance algorithm.



Plates of Komokiacean Foraminifera from NE-Atlantic

Plate 1 – “Chain-like” komokiaceans: 1) Chain sp.1 - 2) Chain sp.2 - 3) Chain sp.3 – 4) Chain

sp.4 – 5) Chain sp.5 – 6) Chain sp.6 – 7) Chain sp.7

Plate 2 - Komokia-like group: 1) Komoki sp.1 – 2) Komoki sp.2 – 3) Komoki sp.3 – 4) Komoki

sp.4 – 5) Komoki sp.5 – 6) Komoki sp.5-bis – 7) Komoki sp.6 – 8) Komoki sp.7

Plate 3 - Lana group: 1) Lana mudball – 2) Lana sp.1 or Cerebrum (Schroder) – 3) Lana sp.2 –

4) Lana sp.3 – 5) Lana sp.4 – 6) Lana sp.5 – 7) Lana sp.5a – 8) Lana sp.6

Plate 4 – Other Komokiacean Foraminifera: 1) Ipoa spp. – 2) Septuma spp. – 3) Reticulum sp.1

– 4) Edgertonia argillispherula – 5) Edgertonia floccula – 6) Mudball Komoki sp.2 – 7) Mudball

Komoki sp.3 – 8) Mudwall Crithionina spp

Plate of Komokiacean Foraminifera from Weddel Sea

Plate 5 – Other Komokiacea Foraminifera: 1) Ipoa spp. – 2) Septuma spp. – 3) Normanina spp. –

4) Edgertonia spp.– 5) Saccorhiza spp.

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A b y s s a l P

l a i n

I b e r i a

n

A b y s s a l P

l a i n

Figure 1. - Location Map



Phylogenetic Tree - sF1-sB primers

0.034Epistominella

Anna4941

SV2647 Reophax

RIS3889RIS3883 3SV E9 R.scorpiurus1398 Reophax

Anna 4945A68 231 ReophaxA324 241 ReophaxRIS3884

12121018 Psammosphaera

TB3929 PsammosphaeraA26 Silver

W274 SaccamminaRIS3907 silver

TJ528 H.albaGU1764 H.alba

K33 Cylind

3999 213 Dunstaff GU1780 argenteus

JP M5GU1784 B.flexilis4004 226 Dunstaff

EdaphoallogromiaAnna 4951

AllogromAA.latticolaris

GU1760a4006 228 Dunstaff GU1760 B.minutaA2919 Hyperammina

A1037_CrithioninaW37a VanhoeffenellaAnna4947

W178 Vanhoeff SV2857 H.hirudineaA1157 H.hirudinea

BoderiaAnna4943RIS3923 Q Komoki

GU1776 P.aurataJP M31

HAB CR2 3cl

A1124 HippocrepinaJP P4Anna3502 B

QuartzballNotodendro

1045 Rhabdammina1439 H.bradyi

SV2844 mudball2359 Psammophaga

K51 P.simploraTB3790 Psammophaga4023 262 Dunstaff

TJ563 Saccodendron

TJ547 ArmorellaA.raraA.triangularis

613 Reticulomyxa

Lana sp.1

Komoki sp.3

Normanina

Chain sp.1

Reophax spp.

Epistominella exigua



0.026

EpistomineAnna4941

Sv2647 ReophaxA68 231 ReophaxA324 241 ReophaxRIS38841212

1018 Psammosphaera

RIS38891398 ReophaxAnna4945

SV E9 R.scorpiurusTb3929 Psammosphaera

Gu1780 argenteusJP M5Gu1784 B.flexilis4004 226 Dunstaff

Anna3498 17Anna3496.1 17Anna3496.2 17

Anna3455.4 17Anna3397.4 17Anna3455.3 17

Anna3455.6 17SV2841Sv2840 10

W274-SaccamminaA26 Silver Tj528 H.albaGu1764 H.alba

Anna3502 B

Anna3502 17k33-Cylind3999/213/Dunstaff

RIS3923 U2Anna3315 17

A2922 TinogullmiaAnna4943

BoderiaRIS3923/Q/Komoki

GU1776_P.aurataJP M31

Quartzball Notodendro

1439 H.bradyi1045 Rhabdammina

Sv2844 mudballEdaphoallogromia

Anna4951

AllogromAA.latticolaris

4006/228/Dunstaff GU1760aGU1760-B.minutaA2919 Hyperammina

A1037 CrithioninaW37a VanhoeffenellaAnna4947W178 Vanhoeff 2359 Psammophagak51-P.simplora

Tb3790 Psammophaga4023/262/Dunstaff Anna3474 17

A.raraA.triangularis

Tj563 SaccodendronTj547 Armorella

Sv2857 H.hirudineaA1157 H.hirudinea

Anna3310

A1124 HippocrepinaJP P4

613 Reticulomyxa

Lana-like, Antarctica

Contaminants, Antarctica

Lana sp.1, NE Atlantic

Normanina, Antarctica

Chain sp.1, NE Atlantic

Komoki sp.3, NE Atlantic

Normanina, Antarctica

Lana-like, Antarctica

Phylogenetic Tree - sF1-s17+sB primers

Epistominella exigua, NE Atlantic

Reophax spp. , NE Atlantic



1 2

3 4

5 6

7

Plate 1 - “Chain-like” komokiaceans



4

3

5

6

7

8

Plate 2 - Komokia-like group



1 2

3

4

5 6

7

8

Plate 3 - Lana group



1

2

3

4

5

6

7

8

Plate 4 - Other Komokiacea Foraminifera



Plate 5 - Komokiacean Foraminifera from Weddel Sea

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3

4 5

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